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This will be an index of issues with R1 anime releases over the years. Note that this will list only issues with DVDs and Blu-rays, and not VHS and Laserdisc releases. Links will be provided whenever possible. If you're aware of an issue not on this list, please bring it up so I can add it! I'm doing this so people can easily find these issues, and newer fans are made aware of these should they choose to buy any affected release.

General Issues:
-R1 releases will be brighter/darker than JP releases at times, and will also have some color issues. Also R1 releases generally have inferior video quality compared to the Japanese releases, though there are instances where the R1 release is of higher quality than the Japanese one.
-FUNimation releases prior to 2009 had alternate-angles in order to show the original Japanese credits and eyecatches, and the English-translated credits and eyecatches. This greatly affected the video quality in a bad way. Re-releases with alternate-angles dropped had significantly improved video quality. Relevant ANN Answerman article: Why Do Older Funimation DVDs Have Multi-Angle Credits?
-Many releases will be missing music/won't have them subtitled due to rights issues. The Japanese music industry can be very difficult to deal with, so these issues are most of the time understandable, and people shouldn't hold it against the R1 companies.
-Since the release of Yosuga no Sora in May 2015, Media Blasters DVD titles are released on DVD-Rs, and any reprints of catalog titles will be on DVD-Rs. Some reprints of older releases will have a combination of pressed discs and DVD-Rs. Their Blu-ray releases are pressed, and are not on BD-Rs.

Two things I felt like noting as well in regards to extras...
-Aniplex USA releases will exclude content from the Japanese release, be it physical extras, booklet pages, and/or video extras. On their imports except the $400 Garden of Sinners LE Blu-ray and Persona 5 the Animation: The Day Breakers Blu-ray, special features are not subbed. Also, they'll post some of that content and other content on their YouTube channel when it should be on the Blu-rays themselves.
-R1 releases will be missing physical extras from the Japanese release, particularly releases after singles died. Also many video extras will be missing.

For a list of issues with FUNimation releases, please see the following post for now.
http://myanimelist.net/blog.php?eid=779846

Also, here's two useful links leading to Blu-ray caps on various releases. You can also check Blu-ray.com for caps as well if they've reviewed a title.
https://web.archive.org/web/20140406204711/http://muhootsaver.tistory.com/notice/1294
http://forum.blu-ray.com/showthread.php?p=12150158#post12150158

Other Relevant Blog Entries
R1 Releases Missing Extras From Other Releases
R1 Releases Missing JP Extras
This Is How You DON'T Translate Anime

Last updated: 6/10/2016

Bludgeoning Angel Dokuro-chan Media Blasters Special Edition DVD
The hubs are not reliable, and the discs can arrive loose.
https://twitter.com/BigOnAnime/status/544684916353814528
[The disc did play properly for me from beginning to end, thankfully.]

Blue Submarine No.6 Bandai and Discotek Releases
The Bandai releases have very bad video quality, and are inferior to the Japanese Blu-ray despite it being a Q-TEC upscale.
http://forum.blu-ray.com/showthread.php?p=12568516#post12568516
The issues with the Discotek DVD AND Blu-ray is they accidentally released the edited version of the English dub.

Colorful: The Motion Picture Sentai Filmworks Blu-ray
Towards the end of the film the video quality tanks.
http://www.fandompost.com/oldforums/showthread.php?19122&p=184338&viewfull=1#post184338

Crest/Banner of the Stars I & II Bandai DVD's
There are numerous translation errors.
http://www.fandompost.com/oldforums/showthread.php?23900&p=198791&viewfull=1#post198791

Dragon Ball FUNimation Blue Bricks DVDs
The video is slightly zoomed-in on the Blue Bricks.

Dragon Ball GT FUNimation Green Brick DVDs
FUNimation's Green Bricks releases suffer from DNR.
http://www.kanzenshuu.com/forum/viewtopic.php?p=218256#p218256
http://www.kanzenshuu.com/forum/viewtopic.php?p=215181#p215181

Dragon Ball Z FUNimation Orange Brick DVDs and Season Set Blu-rays
The Orange Brick Season Sets as well as the Season Set Blu-rays (NOT to be confused with the Levels, the only issue those had was some black crush, and no next episode previews (both of these releases suffer that same issue of no NEPs) crop the show from 4:3 to 16:9, oversaturate the colors, and apply very heavy DNR, which actually ripped away footage in the Orange Bricks due to the DNR being way too strong. The Blu-rays do the cropping via pan-and-scan. The later Orange Brick Season Sets do later-on retain the film grain and stop the oversaturating of colors, leaving only the cropping as the only remaining issue.
https://www.youtube.com/watch?v=oSLnUpkTsv8
https://www.youtube.com/watch?v=ulY2c5EPdB8
http://www.kanzenshuu.com/forum/viewtopic.php?p=739310#p739310

Some things also worth noting: The Dragon Boxes are currently the best complete release of the series, but are unfortunately permanently OOP. Due to a lack of color correction by Toei Animation, many colors are wrong. For instance, Bulma's hair is greenish, the sky is greenish, and skin tones are pinkish in many episodes. Also the Japanese audio will forever have issues due to Toei tossing out the master audio tapes.
https://www.youtube.com/watch?v=WA1St_lORuM

Elfen Lied ADV Films Blu-ray
The English audio is muffled, except on the OVA. The issue also affects the OP/EDs despite those being in Japanese. Listening to the OP/ED on the Japanese track is fine, but when you switch the audio to the English dub, it sounds muffled by comparison. This issue affects only the Blu-ray and no other ADV Films release of Elfen Lied.
http://www.fandompost.com/oldforums/showthread.php?22056&p=204331&viewfull=1#post204331
https://www.youtube.com/watch?v=-H0vJCR0o_w

Full Metal Panic! Fumoffu ADV Films DVDs
All of the ADV releases of Full Metal Panic! Fumoffu are plagued with dot crawl due to Kadokawa providing them composite masters. The FUNimation releases are not affected by this, and have clean video.

Fushigi Yûgi Media Blasters DVDs
The hubs are very unreliable, and the discs popout frequently.
https://www.youtube.com/watch?v=1TcI1gGS2ew
http://www.amazon.com/product-reviews/B0076YFJHM/ref=cm_cr_arp_d_viewopt_sr?ie=UTF8&showViewpoints=1&filterByStar=critical&pageNumber=1
http://www.amazon.com/product-reviews/B008U1AOKM/ref=cm_cr_arp_d_viewopt_sr?ie=UTF8&showViewpoints=1&filterByStar=critical&pageNumber=1
http://www.fandompost.com/oldforums/showthread.php?8320&p=112875&viewfull=1#post112875

Girls Bravo Geneon AND FUNimation DVDs
Both the Geneon and FUNimation DVDs of Girls Bravo are plagued with dot crawl due to Kadokawa providing composite masters.

Ghost in the Shell 2.0 Manga Blu-ray
The Blu-ray includes the original version of the movie, but as a special feature, and is upscaled.
http://forum.blu-ray.com/showthread.php?p=2489445#post2489445

Ghost in the Shell: 25th Anniversary Edition Manga Blu-ray
The English audio is missing lines and sound effects present on the DVD releases. It also suffers from an inferior translation.
http://www.fandompost.com/oldforums/showthread.php?32587&p=269348&viewfull=1#post269348

Horizon in the Middle of Nowhere Sentai Filmworks Blu-ray
Half of episode 7's video quality looks absolutely terrible. The complete collection re-release fixes this problem.
http://www.fandompost.com/oldforums/showthread.php?6096&p=145470&viewfull=1#post145470
http://oi63.tinypic.com/1rzvjm.jpg
http://oi68.tinypic.com/2pytf6g.jpg
http://oi63.tinypic.com/1z4izw0.jpg
http://oi66.tinypic.com/153l1jc.jpg
http://oi63.tinypic.com/oi7qk3.jpg
http://oi66.tinypic.com/bgabo4.jpg

Kids on the Slope Sentai Filmworks Blu-ray
The initial pressing of the Kids on the Slope Blu-ray suffered from an audio quality issue on the Japanese audio during episode 11. The issue caused all of the dialogue to be stuffed into the left speaker. A replacement program was announced.
http://www.fandompost.com/oldforums/showthread.php?10412&p=178061&viewfull=1#post178061
http://www.animenewsnetwork.com/news/2013-05-06/retailer/sentai-filmworks-recalls-kids-on-the-slope-bd-release

Koe de Oshigoto! Media Blasters DVD
The disc goes back to the menu after each chapter, and is plagued with various subtitle issues.
http://www.fandompost.com/oldforums/showthread.php?23188&p=243358&viewfull=1#post243358
http://www.fandompost.com/oldforums/showthread.php?23188&p=247202&viewfull=1#post247202

Magic User's Club Media Blasters DVDs
The Media Blasters releases of Magic Users Club TV and the OVA featured mono audio on many of the English dub episodes. The Nozomi Entertainment releases fixed this problem.

Martian Successor Nadesico ADV Films DVDs
ADV Films accidentally released the TV version of the show. This led to the Nozomi Entertainment release to not sync up with the ADV dub as the release was sourced from the Japanese Blu-rays.
https://fandompost.vbulletin.net/forum/anime-manga-discussions/us-blu-ray-dvd-and-simulcast-industry-news/11865-rightstuf-nozomi-ent-licenses-martian-successor-nadesico?p=243887#post243887
http://catsspat.dyndns.org:2080/anime/Nadesico/DND-001/index.html
http://catsspat.dyndns.org:2080/anime/Nadesico/KIBA-91311/index.html

Mawaru Penguindrum Sentai Filmworks Blu-rays
The Sentai Filmworks parts suffer from severe video quality issues, and apparently translation errors. As of this blog post, Sentai Filmworks still has not released a complete collection set with these issues fixed.
http://www.fandompost.com/oldforums/showthread.php?14291-Sentai-Filmworks-licenses-Penguindrum&p=154810&viewfull=1#post154810

Moribito: Guardian of the Spirit Blu-rays (VIZ AND Media Blasters)
Both the VIZ Media and Media Blasters releases suffer from video quality issues, the Media Blasters one in particular, which is vastly inferior to the Japanese Blu-ray Box.
http://www.fandompost.com/oldforums/showthread.php?27749-Viz-Media-acquires-Moribito-Guardian-of-the-Spirit/page9&p=264105#post264105
http://www.fandompost.com/oldforums/showthread.php?27749-Viz-Media-acquires-Moribito-Guardian-of-the-Spirit&p=267740&viewfull=1#post267740
Media Blasters even tried to defend the problems with their Blu-ray release.
http://www.fandompost.com/oldforums/showthread.php?849-Moribito-Guardian-of-the-Spirit&p=25210&viewfull=1#post25210
http://www.fandompost.com/oldforums/showthread.php?849-Moribito-Guardian-of-the-Spirit&p=25461&viewfull=1#post25461

My-Hime Bandai Singles
The My-Hime Bandai Entertainment singles were plagued with glitches, not working on many DVD players.
https://twitter.com/NJ_/status/547162624585379840

Nura: Rise of the Yokai Clan VIZ Media Blu-ray
The video quality is absolutely atrocious.
http://www.fandompost.com/oldforums/showthread.php?12584-Nura-Rise-of-the-Yokai-Clan&p=174914&viewfull=1#post174914

Nura: Rise of the Yokai Clan: Demon Capital VIZ Media DVD's & Blu-rays
VIZ Media released the TV version of the show. No real explanation as to why was given.
http://www.animenewsnetwork.com/news/2014-03-16/viz-acknowledges-its-nura-release-uses-tv-version

Papillon Rose Maiden Japan DVD
The Maiden Japan release uses composite masters, is plagued by dot crawl, is apparently sourced from the TV version, and has music rights issues.
http://web.archive.org/web/20111004202407/http://www.mania.com/aodvb/showthread.php?t=100801

Ranma 1/2 Set 1 VIZ Media Blu-ray
The first disc of the first Blu-ray contains minor ghosting, but only on the OP. This does not affect any other set or disc.

Sailor Moon VIZ Media Blu-rays
The video quality is absolutely atrocious, and VIZ Media lied about many things.
http://www.amazon.com/gp/customer-reviews/R123Y8PP112G85/ref=cm_cr_pr_viewpnt?ie=UTF8&ASIN=B00M0ETRHG#R123Y8PP112G85
Also there were replacement programs on some things. Sailor Moon R: Part 1 Limited Edition had a printing error, and was missing the inside artwork on some sets. Sailor Moon R: Part 2 had an audio timing issue.
http://www.animenewsnetwork.com/news/2015-07-22/missing-sailor-moon-r-set-1-reversible-covers-to-receive-free-replacements/.90733
http://www.fandompost.com/oldforums/showthread.php?31509-Viz-Media-licenses-Sailor-Moon&p=334272&viewfull=1#post334272
http://www.viz.com/node/1006268

Samurai Champloo 1st Geneon/FUNimation Blu-ray
The first Blu-ray release of Samurai Champloo suffered from DNR and video quality issues. The Anime Classics re-release fixed these problems.
http://www.blu-ray.com/movies/Samurai-Champloo-Complete-Series-Blu-ray/6686/#Screenshots

Scrapped Princess Bandai DVD's
The Bandai Entertainment release of Scrapped Princess is plagued with very bad dot crawl due to Kadokawa providing composite masters.
http://www.animenewsnetwork.com/bbs/phpBB2/viewtopic.php?p=4840500#4840500

Squid Girl Media Blasters Part 1 DVD
The hubs for this release were very unreliable, and the discs would frequently popout.
https://youtu.be/BRhlEPQHN4I?t=3m10s
https://youtu.be/j_jru6TmUm8?t=4m20s
https://youtu.be/t5MnDjd3T8I?t=4m40s
http://www.amazon.com/product-reviews/B0057FGD5E/ref=cm_cr_arp_d_viewopt_sr?ie=UTF8&showViewpoints=0&pageNumber=1&filterByStar=critical

Super Robot Wars OG: Divine Wars Media Blasters DVD's
The MB release has multiple video and audio issues.
http://www.fandompost.com/oldforums/showthread.php?19838-Media-Blasters-licenses-Super-Robot-Wars&p=245641&viewfull=1#post245641

The Vision of Escaflowne Bandai DVD's
Bandai Entertainment released the TV version of Escaflowne. This meant that certain scenes were cut out as the Japanese TV broadcast had some content cut out due to time issues. The missing scenes were restored on the Japanese home video releases.

Trigun FUNimation and Geneon DVD's
(I've slightly edited the quote to make it more accurate.)The same situation applies to FUNimation's releases, their first release had only the first version of the OP, however the Anime Classics release fixed this. FUNimation's releases also have worse video quality than even the original Geneon singles from 2000. Some comparisons against the Madman and Japanese release below.
http://screenshotcomparison.com/comparison.php?id=81889
http://screenshotcomparison.com/comparison.php?id=81767

Vandread FUNimation DVD's
FUNimation's releases of Vandread have worse video and audio quality compared to the Geneon releases, and also feature some odd video anomalies.http://www.fandompost.com/oldforums/showthread.php?37582-Upgrading-my-old-ADV-DVDs&p=276737&viewfull=1#post276737

Vampire Hunter D: Bloodlust Discotek Blu-ray
The contrast for the Urban Vision DVD is better than the Discotek Blu-ray. Unfortunately due to how it was produced, it's unlikely it'll see a proper release.
http://forum.blu-ray.com/showthread.php?p=11280197#post11280197
http://forum.blu-ray.com/showthread.php?p=11309675#post11309675
http://forum.blu-ray.com/showthread.php?p=11309937#post11309937

Yamibo Media Blasters DVD
While other DVD-R releases from Media Blasters worked on PlayStation 3 consoles, this release does not. Media Blasters also made it clear they would not fix the issue by telling people to use a computer or another player. In addition to this, they also released the TV version of the show.
http://www.fandompost.com/oldforums/showthread.php?21847-Media-Blasters-Acquires-Yamibou&p=358010&viewfull=1#post358010
http://www.fandompost.com/oldforums/showthread.php?21847-Media-Blasters-Acquires-Yamibou&p=358156&viewfull=1#post358156
http://www.fandompost.com/oldforums/showthread.php?21847-Media-Blasters-Acquires-Yamibou&p=358244&viewfull=1#post358244

Yosuga no Sora Media Blasters DVD
In addition to being on DVD-R's, this release also has a very low bitrate and poor video quality, and other issues.
http://www.fandompost.com/oldforums/showthread.php?29657-Media-Blasters-licenses-Yosuga-no-Sora&p=315365&viewfull=1#post315365
http://www.fandompost.com/oldforums/showthread.php?29657-Media-Blasters-licenses-Yosuga-no-Sora&p=315049&viewfull=1#post315049

[Work in progress]