TMS Entertainment's early anime Chingo Muchabei counts as this. The show was being made when color television became the standard over black and white, and by the time it was ready to air in 1968, the network put off airing it, in favor of color shows (the irony being that the same network aired two more black and white anime from TMS after Muchabei was finished). The show finally did air, in 1971, and it was rushed through to get every episode broadcast in a month and a half. As a result of this, Muchabei ended up being the final black and white anime to air, even if it wasn't the last one produced.
Code Geass's first season. Sunrise was wary of trusting a full series to director / co-creator Goro Taniguchi, thanks to his reputation for perfectionism and his other quirks, so he was only handed 25 episodes to begin with. The staff often had to piggyback off of other parts of the studio that were working at the same time (for example, the Geass staff didn't even have their own photocopier) and the writers were only three or four episodes ahead of the broadcast, about half the "buffer" that most series have. When the series became a runaway success, things went much better, but fans tend to blame the series' being split in half for the perceived drop in quality in the second half.
The three Latin American Spanish dubs of Detective Conan have had lots of messes in their productions:
According to the people who worked in the first dubbed version (from the first to the fifth season), which was dubbed by VDI - Point.360 in Los Angeles, California, the entire dub was a complete mess from the start, since many episodes were dubbed in the same day and sometimes by five different voice directors, who normally ignored what the other director did in the previous episodes they dubbed before causing regular characters, like Sonoko Suzuki, to get her name changed in almost every episode she appeared. This and the series suffering low ratings were the reasons why the series was canceled in Latin America, despite its Cult Classic following.
The two first movies were dubbed in Mexico, and while the acting itself was pretty good, the translation was awful, since it not only suffered from the Too Long; Didn't Dub trope (something that rarely happens in a Mexican Spanish dub), it was later found out the Mexican dub illegally used a plagiarism script from a fansub for the translation, causing a quite embarrassing incident with both the fans and the Japanese licensors, and losing the rights to dub any related material regarding the series. The ban was only lifted in 2016, when another Mexican dub company got the rights to dub the 18th movie (Dimensional Sniper) and one of the crossovers with Lupin III for a digital release, and the 19th movie (Sunflowers of Inferno) for a theatrical release.
After the incidents with both the Hispanic and Mexican voice actors teams, the series was dubbed for good (from the sixth season onwards) in Chile instead, after a Chilean TV channel specifically bought the rights of the series and the movies due to older Chilean fans's love of the franchise. The ironic twist of this, at least in the Chilean Spanish dub of The Last Wizard of the Century, is that this version also has a plagiarized script from a fansub - except, unlike with the Hispanic and Mexican cases, it only happens in the subbed version. Whoopsie?
The Dream Machine, the final movie of the lateSatoshi Kon, has experienced its share of trouble, having gone from production into Development Hell, back into production only to fall back into development hell. First Kon's death from pancreatic cancer put the film on hold to determine the next course of action. Kon's widow and Studio Madhouse's Masao Maruyama said they would finish the film and production resumed. However, at Otakon 2011, Maruyama reported the movie has been put on hold due to financial difficulties. Maruyama is still determined to finish the film eventually, with about 600 shots out of 1500 had been animated at that point.
The Fruits Basket anime was full of this, as Natsuki Takaya not only was more involved than other authors in it, but she had huge Creative Differences with the director Akitarou Daichi. This is cited as the reason why there is no second season, despite the series' popularity and its open ending.
Mobile Suit Gundam SEED Destiny also suffered this, partly because of head writer Chiaki Morosawa's battle with cancer during production, which resulted in her turning in scripts in late, which necessitated the numerous clip shows throughout the series. Secondly, although Shinn was supposed to the main character of the series, Kira was thrust back into the spotlight from episode 39 onwards, because of his popularity with the Japanese audience. Finally, there was director Mitsuo Fukuda being demanding on the voice actors on the way how they're supposed to to be portrayed (specifically, Naomi Shindo [the voice of Cagalli] and Maaya Sakamoto [the voice of Lunamaria]). This was confirmed by Rie Tanaka (the voice of Lacus and Meer) at her 2008 New York Anime Festival appearance, as well as Kenichi Suzumura (the voice of Shinn) in one of his Twitter posts.
Hols: Prince of the Sun was being made when Toei was restructuring itself to focus more on cheaper productions over lavish animations, and when its animators were starting to unionise. By coincidence, most of the aspiring, "troublesome" pro-union animators were assigned to work at the studio focusing on lavish animations, one of which was Hols. Originally intended to be a two-hour epic, the film was cut down to just 80 minutes as it exceeded its then-standard eight-month production period. When the film was finished, Toei did very little advertising and gave it a theatrical run of only ten days. At the end of it all, Isao Takahata was demoted, told he would never direct again, and Hols became an influential classic widely hailed as one of the best anime ever created.
Hyouge Mono had a few cases of some behind the scenes drama. It started with the band member of cro-magnon which co-composed the music and wrote the theme song getting arrested on a drug charge suspicion then the original author and the editorial staff walking off the project and asking for a credit change from Original Creator to Original Concept.
Koe no Katachi deals heavily with ableism in Japan. There were legal disputes over publishing and there was difficulty getting someone to publish it period. The original one-shot was created all the way in 2008 but the most common version is from 2011. It took another two years for it to become a proper series.
Lost Universe is a notorious case. The show's budget was already low, but a studio fire resulted in lots of work from the first few episodes destroyed. They had to be reanimated on an even lower budget by a South Korean studio while the rest of the show resumed production. This all occurring during a recession. One episode looked so bad on TV, that it had to be almost entirely re-animated again for home video and re-runs. A second season was also canceled so the studio could make way for more Slayers movies.
For a long time, Mahou Sensei Negima! looked like a happy subversion. Ken Akamatsu wanted to do a shounen-action series from the start, but his producers wanted a harem show like his extremely popular Love Hina series. Akamatsu faked a harem series, using the first two volumes to lay down characterization, then slowly segue into the fighter series he wanted from the start. This resulted in an extremely intelligent and popular series known for its Amazon Brigade and ridiculously badass ten-year old protagonist. However, some three hundred chapters later, the executives tried to take the rights to the series away from him. He responded by ending the series abruptly, with a carefully crafted final chapter that managed use the "Where Are They Now?" Epilogue to make sure no one else could use his series. It remains to be seen if there will be any more releases filling in the unanswered questions.
Nadia: The Secret of Blue Water oh so much. Aside from the unexpected decision to extend the show to 39 episodes (hence the Korean-animated filler arc - so detached from the rest of the show that even director Hideaki Anno declared it all but episodes 30 and 31 non-canon), there were other problems plaguing the show's production progress. Anno reportedly disliked the original script for the show, and decided to rewrite it from scratch. Furthermore, any "suggestions" from NHK on how to "improve" the show were instantly disregarded, hence the Darker and Edgier tone for most of the canonical episodes. Because of Anno's demand for perfectionism, many episodes ran late, with Anno spending more than eighteen hours per day on the show! At one point, after episode 20 was broadcast, it took an entire month for audiences to see the subsequent one. The budget for the show also caused Gainax to lose more than ¥800 million (half a million dollars!) in finances. They were also denied any of the rights. Perhaps because of this, neither Gainax nor NHK worked together on another show. Nadia is also often pointed to as the cause of Anno's depression and breakdown leading to .....
The third Rebuild of Evangelion movie was hit with this was well. In addition to massive script rewrites and some very unpopular creative decisions, Anno had anotherCreator Breakdown while working on it. In interviews, he revealed that working on the series again had brought back his serious bouts with depression, and that he'd often go for long periods of time without even showing up to the studio. He credits his friend Hayao Miyazaki and working on Shin Godzilla for helping him through this troubled period and his eventual Creator Recovery.
The English dub for Evangelion 3.33 has suffered its own share of problems. Funimation had originally announced that that the dub would be released on DVD in February 2014, but Anno's apparent dissatisfaction with the job they did led the company to re-record the entire thing and push back the release date to February 2, 2016.
The fourth and final Rebuild film currently appears to be in Development Hell, with its release date (initially in 2013) being repeatedly pushed back or revised. It is currently on hiatus while Anno directs the new Godzilla film.
Puella Magi Madoka Magica: The series had just aired its 10th episode when the March 2011 earthquake and tsunami hit Japan. Most shows held back a week out of courtesy, but while most shows were returned the following week, Madoka Magica wasn't. Despite using the time to polish up the final two episodes, the channel that had first air rights to the series refused to air it for nearly two months before relenting and airing the last two back to back.
In certain locations the 10th episode was also delayed (though there was an internet livestream on Nico Nico Douga) and was aired with the other two episodes. Note that none of this seemed to hurt the ratings (there was even a newspaper advertisement for the last two episodes) and the episodes even managed to have a Meaningful Release Date.
Urobuchi originally wanted things just to end with The Rebellion Story. This was denied, and while it helps that he gladly embraced the alternate ending suggested to him for that installment, he has considered just leaving, claiming to lose control over the franchise.
The original DiC/Cloverway English dub of Sailor Moon is the only English anime dub with an entire book written about its production.
The show was licensed by DiC following a lengthy bidding war with Toon Makers who wanted to remake the show entirely (producing Toon Makers Sailor Moon). Once they did finally get it, they didn't know what to do with it since they mistakenly assumed they were only distributing it in North America and that an English-language adaptation was already produced. Due to their lack of knowledge of Japanese animation, Carl Macek was originally hired to write the adaptation, but was fired early in production due to Creative Differences with Andy Heyward (DiC's then-CEO). Fred Ladd (a veteran of English anime dubs, with experience going back to Astro Boy and Kimba the White Lion) was then hired.
On the recording side of things, Optimum Productions, a Toronto-based dubbing company, was selected to record the dub, however they ran into issues early on. Tracey Moore, the original ADR director and voice actress for Sailor Moon, quit after 13 episodes due to stressful Creative Differences and was replaced with Roland Parliament as director and Terri Hawkes as voice actress (also, Rino Romano quit his role of Tuxedo Mask around this time as well). Production was so far behind schedule, Hawkes began recording the night she was cast and ended up recording entire episodes in one take. Parliament worked long hours into the night, often slept at the studio, and became ill during production. He also had to deal with angry executives with DiC, who complained about the actors' Canadian accents and told him that the show was "not for fucking Canadians. It's for fucking Americans."
DiC themselves were also at the mercy of Toei in Japan, who had to approve of each and every change made, often without consulting the series' creator, Naoko Takeuchi. The episodes were on their air only a couple weeks after being recorded, with 65 episodes being dubbed in three months.
It was canceled on a cliffhanger and couldn't continue at all until 1997 when YTV in Canada and Irwin Toy paid to fund more episodes to give it some closure, with Pioneer funding dubs for the movies. For these, Parliament was fired over Creative Differences within Optimum and replaced with John Stocker, who was also fired later on. The voices for Sailor Mars and Tuxedo Mask were also recast (though Mars later returned), and Fred Ladd was replaced with writers at Optimum.
S and SuperS had it worst though. DiC declined to license more episodes, so Cloverway (Toei's then-US branch) stepped in after YTV and Cartoon Network ordered more episodes. Cloverway gave Optimum almost complete creative freedom as long as 77 episodes were recorded in four months. This resulted in many voice actors not returning (including Terri Hawkes, who went on maternity leave) and replaced with poor substitutes. Production was so rushed, that as many as 11 episodes were recorded in each 4-hour session with the voice actors recording each line only twice, with the better take used. In addition, the new voice director, Nicole Thuault, could not speak English (only French) and was a Prima Donna Director to boot, and relied on an interpreter to communicate with the actors. The writers at Optimum all worked independently without any kind of "bible" on what the attack names, transformation phrases, etc. were supposed to be, resulting in them changing many times throughout these episodes. Fans could usually tell which writer wrote which episode based on the terminology used.
All of this contributed to an extremely messy dub that's very polarizing to this day. The dub didn't even cover the final season due to the franchise's legendary legal issues. It's now being replaced with a newer faithful dub from Viz Media and Studiopolis with a more normal production.
Super Dimension Fortress Macross had shades of this trope. Originally envisioned for 48 episodes when the show was first greenlit, one of the financial backers went out of business, forcing a cut to 23 episodes when a new backer was found but did not have the money to fund the original 48. But the show was a hit upon premiere. And so, to bump the episode count up, they brought in legendary production company Tatsunoko. They foisted upon Studio Nue a host of questionable farm studios who brought in Off Model work, and even at one point managed to get a nearly-completed episode left on a train, nearly forcing a complete redo of the entire episode. And then, the fact that Macross was a hit and the interesting financial situation between Big West and Tatsunoko caused the production to be troubled long after the last episode went off the air. Even the title was due to Executive Meddling, as one of the producers, an admirer of Shakespeare, wanted the show to be called Macbeth, and had to be negotiated down to Macross as a compromise.
American fans were thrilled when FUNimation got a hold of the 3rd Tenchi Muyo! OVA series. However, Funimation screwed up the contract and only got the rights for the first three episodes. It took a year to renegotiate for the other four episodes and get them out, barely averting a case of The Other Darrin when voice actor Bob Papenbrookpassed away soon after the release of the series.
This trope already occurred when they got back the entire voice cast... except Ryoko, arguably the most popular character in the show. While the details of what happened are kept private, her original voice actress, Petrea Burchard, simply said "we just couldn't work it out." This change remains one of the more controversial aspects of the OVA.
The Vision of Escaflowne television series went through several years of Development Hell, in which time the attendant manga series based on pre-production materials was being published, and by the time the series itself made it to air they had to abruptly cut down the plot from their planned 39 episodes to 26, resulting in a very rushed ending that lacked much closure and left several plot threads hanging.
Yu-Gi-Oh! 5D's had this creep up in the post Dark Signer seasons. Among the issues that came up included extensive Executive Meddling from Konami to promote certain cards, staff being taken off to work on the 10th anniversary movie resulting in a lot of filler to wait for them to be back for the big plot episodes, and real life issues that ranged from the major female character's actress having to take time off to be married thus demoting her to extra, to another female character's voice actor being fired after, of all things, being linked to a cult that forced the series to also remove any and all supernatural elements from the series. The later series in the franchise Yugioh Arcv had some of the same issues with a V.A causing a major character to appear sporadically and movies taking talent away throwing off schedules, though so far no cult problems.