To begin with, it had a deadline that was far too short—production began in May 1938, and it was due Christmas 1939; this is less than half of the four years of production that went into Snow White and the Seven Dwarfs, the film it was meant to emulate to begin with.
A studio that was under equipped to take on the challenge of making a Disney-like feature length animated film (many of the staffers weren't familiar with the West Coast style of animation pioneered by Disney), not helped by an influx of East Coast and West Coast staffers who were at odds with each other on their approaches to animation, and the studio's decision to hire amateur, apathetic Miami art students, as well as newcomers who received a few hours' worth of cram-course art trainingnote contrast this to the years of extensive art training and schooling Disney and Don Graham pushed upon their artists resulted in sloppy inking and bad in-between work (explaining the film's very uneven animation quality). The Fleischers' move to a new studio in Miami also resulted in many of their talented employees in New York getting left behind (including Betty Boop voice actress Mae Questel), with the few who did make the move becoming homesick, as well as putting up with the hazards and quirks of Florida (such as many mosquito infestations).
A feud between story artists over which direction the story would take—it was planned as a Bing Crosby vehicle at one point, and at one point Popeye was intended to be the star of the film, with its tone being more cartoony, as Max Fleischer actually did not wish to follow the Disney approach to animated films. Both of the previous stories were thrown out and rewritten by West Coast storymen, particularly ex-Warners staffer Cal Howard.
A feud between Max and Dave Fleischer themselves over whether Dave himself or another person would compose the film's score.
The fact that the film was being made in the Fleischers' new studio in Miami, Florida (which was far too small to hold the 700+ staffers needed to complete Gulliver) meant that if any equipment broke down, it would have been very difficult to get it fixed in any reasonable time. The lack of film industry in Miami also meant that, unless they wanted to use local actors or their woefully inadequate amateur orchestra (which was impeding the sound quality of the shorts from mid-1938 onward), they had to outsource recording sessions to West Coast studios (which they did for Gulliver, Mr. Bug Goes to Town, and the Superman Theatrical Cartoons).
In the end, while the film did modestly well at the box office, Paramount deliberately discounted the money the film made in Europe before World War II broke out there, meaning the film had much overhead left to be paid, leaving the Fleischers in the red. Critical reaction was also mixed, with a cruel remark from rival Walt Disney quipping "We can make a better film than that with our second-string animators".
The very first Toy Story was subject to constant Executive Meddling, pushing to make it more adult and cynical. Pixar, this being their first feature, dutifully followed the notes from the executives, even if they didn't agree with them. When a preview cut was declared unwatchable, Jeffrey Katzenberg, then head of animation at Disney, asked, with some concern, why on earth Pixar had followed all the notes he, and others, had sent. Production was shut down for two weeks, while Lasseter and the others basically rewrote the entire movie, into pretty much what they wanted in the first place.
The Lion King first suffered from lack of internal faith - only up-and-coming animators or people who wanted to do animals picked up the project, with most going to work on Pocahontas instead. One of the directors, Oliver & Company director George Scribner, who had even travelled with the other director Roger Allers and other people to Africa for reference, left as he disagreed on turning the film into a musical while his intention was focusing on the natural aspects. The script was so bad that it needed a reworking with the help of the directors of Beauty and the Beast - and still was being fine-tuned during production, with completed scenes being reanimated due to dialogue changes. And just weeks before release, an earthquake hit Los Angeles, shutting off the studio and forcing animators to finish their work from home. Thankfully it was all worth it in the end.
The Emperor's New Groove started as Kingdom of the Sun, a Prince and Pauper epic directed by Roger Allers. Since the writers weren't very successful in adding original material and test audiences weren't reacting well, another director, Mark Dindal, was hired to see if things evolved. As the deadline got closer and Allers and Dindal were basically working at two movies simultaneously (the former with a drama, and the latter with a comedy), the higher-ups intervened and Allers quit. After a six-month interval where Dindal and some writers reworked the movie, the film became the screwball comedy that eventually saw the light of day. It was all documented in The Sweatbox, a film shot by Trudie Styler (as her husband Sting wrote songs for the movie) that Disney makes sure that never gets released.
Ratatouille was originally developed in 2001 by Jan Pinkava, but Pixar lost faith in Pinkava and ultimately replaced him with Brad Bird.
Bolt suffered from this in spades. The film was originally helmed by Lilo & Stitch director Chris Sanders, who wanted to make another quirky animated family film. To that end, he envisioned American Dog, which followed a popular television star dog named Henry who (after being knocked out and waking up on a train to Nevada) enlists the help of two other talking animals, including a cat and oversized bunny rabbit, to drive him back home (while believing he's still in a television show). The film went through several different cuts (and suggestions from John Lasseter and other Pixar directors on how to improve the film), but Sanders reportedly rejected all of the changes. Lasseter then fired Sanders from the project, and the film was drastically reworked (under a constrained timeframe) into the final product. Tellingly, American Dog is not mentioned anywhere on the film's DVD features, and only receives a passing reference in the making-of book The Art of Bolt.
Brave had title changes, the dismissal of director\co-writer Brenda Chapman, and many scenes being rewritten and\or dropped during production.
Wreck-It Ralph went through a number of problems along the way. Originally planned to have been screened before Tangled, it had went through a number of cancelled and uncancelled calls along the way before finally getting the go-ahead. As well, the many video game companies, (especially Japanese ones), had strict guidelines as to how their characters should act - Nintendo had guides as to how Bowser should drink a cup of coffee, Sega had them reanimate a scene were Sonic loses some rings because they said he could only lose rings if he were hit and the only reason Q*Bert got prominence in the movie was because Namco took offence at Dig Dug being the target.
The film version of Astro Boy managed to go through no less than three different directors, several different writers and a budget that spiraled out of control due to constant production delays. The bottom fell out when the film's production company went bankrupt a few months before opening. The final product manages to show the chaotic production with its unevenness and lack of direction in terms of plot.
Family Dog, a Steven Spielberg produced animated spin-off of Amazing Stories didn't debut until 1992 seven years after the original "Family Dog" episode of Amazing Stories had aired. Only five episodes of the finished product aired.
The pilot episode of The Simpsons, "Some Enchanted Evening" went so badly wrong that it nearly killed the show before it even began. The big problem was that the key members of the production team didn't appear to be talking to each other. Matt Groening and James L. Brooks imagined a show with unique designs and color schemes, but characters who were animated in a realistic way. Animation director Kent Butterworth (and apparently the people at Klasky-Csupo) on the other hand thought it should be animated in a whacked-out, over the top style with little regard paid to keeping the characters on model. And nobody appeared to have told the Korean animators anything at all, meaning they were let loose on the episode with wildly inconsistent results. The end product, while sometimes defended by animation enthusiasts as how the show should have been animated, wasn't what the producers or Fox wanted at all, and the plug nearly got pulled on the series. Fortunately the second episode, "Bart the Genius" did fit what the producers were looking for, and so they reshuffled the episode order and kicked off the series with "Simpsons Roasting on an Open Fire," while "Some Enchanted Evening" got substantially re-animated and booted to the end of the season.
There is a notorious story surrounding the first time the staff saw "Some Enchanted Evening". In one scene, Bart and Lisa watch a Happy Little Elves cartoon. For some reason yet to be determined, Butterworth had decided to have a bear tear off one of the elves's heads and drink its blood. Needless to say, this did not go over well with the production crew.
Food Fight, a film featuring Roger Rabbit-esque cameos by advertising mascots starring Charlie Sheen was trapped in development for 10 years. Originally set for a 2003 release until being delayed to 2005, it became even further delayed when the harddrives containing all the animation files were stolen and the studio had to start all over again on an even lower budget. The final result was finished in 2009, given a small theatrical release and started to emerge direct to video in other markets in 2012.
One of the biggest sources of friction was over censorship. Nickelodeon was always uneasy with the gross-out nature of the show's humor, and shelved one episode, "Man's Best Friend", due to its violent and scatological content. As a general rule, anything that had to do with religion, politics, alcohol, and tobacco was put under a microscope by Standards & Practices; the character George Liquor had his last name removed from one episode and made only sporadic appearances due to opposition from the network, while another episode featuring The Pope removed a cross from his hat and credited the character simply as "The Man with the Pointy Hat".
The show suffered from severe Schedule Slip almost from the start, the result of, depending on who you ask, John Kricfalusi's perfectionism or the constant battles over what was acceptable to air. Nickelodeon had to rerun the pilot episode in order to have something to show in what would've been the second episode's time slot; this helped the show build an audience but killed any hope for syndication. This became a trend; the first season had only six episodes air between August 1991 and February '92.
Feuding between John K. and Nickelodeon over Schedule Slip and censorship came to a head in September '92, in the middle of the second season, when Nickelodeon fired John K. and took over production themselves via the in-house studio Games Animation. The exact circumstances of John K.'s firing are hotly debated to this day; John K. cites his refusal to censor "Man's Best Friend" as the final straw for Nick, while others blame the Schedule Slip. Regardless, this is the moment when many fans claim that the show took a notable downturn in quality, especially given that a good chunk of the staff left in protest at John K.'s firing. Ren & Stimpy finished its second season and ran for a total of three more before it was canceled at the end of 1995 (though one last episode aired on MTV the following year).
Later on, in 2003, John K. relaunched the show as Ren & Stimpy's Adult Party Cartoon, part of an adult animation block on Spike TV. The show once more suffered from Schedule Slip, though the censorship fights at Nickelodeon were inverted at Spike TV; John K. maintains that Spike TV pressured him to turn up the adult content farther than he was willing to go. In any case, the show only lasted two months and seven episodes (the pilot being the previously-unaired "Man's Best Friend") before being canceled, with many fans declaring it Fanon Discontinuity.