The Disney cartoon "The Golden Touch" (1935). Out of dissatisfaction with one of his directors Disney directed it himself. The cartoon was a huge box office bomb and animators were reminded never to speak of it again. Disney too never personally directed a short cartoon again.
Speaking of John K., Billy West does not have fond memories of working on Ren and Stimpy, mainly because John was a tremendous Jerk Ass to him and everyone else working on the show, which is why he didn't come back to reprise his role as Stimpy for the ill-fated Adult Party Cartoon revival.
Chuck Jones once said that if he were allowed to, he would burn the negatives to every Looney Tunes short he made before 1948 (which had slow pacing and were too much like something Disney's animation company would do). The one short that seemed to get the most contempt from him was Elmers Candid Camera.
Carl Barks, Don Rosa and some of the 9 Old Men grew to hate the animated show DuckTales for not being true to the stories that Carl Barks wrote, as well as taking away TMS's time away from Little Nemo: Adventures in Slumberland (in fact, two of them— Frank Thomas and Ollie Johnston— did work on Little Nemo just so that they could work on something that was outside of what Disney was dishing out at the time).
Trey Parker and Matt Stone feel this way about the first three seasons of South Park, as Parker states outright in a 2011 Entertainment Weekly article: "It's just embarrassing to watch". In fact they hate season 2 so much that they didn't even do commentaries on the DVDs like they did for the other seasons.
The only season 2 episode that they even seem to remotely like is "Not Without my Anus", as they cited it as something "weird and different," though most fans don't agree, as it was pointless filler that interrupted the conclusion of the "Cartman's Mom is a Dirty Slut" two-parter, in which Cartman tries to find the identity of his biological father. But it was April Fool's Day when it aired, so it was fitting.
There are reports that John Erwin, the voice of Filmation's He-Man, does not particularly enjoy talking about his time on the show (for what it's worth, these come not from co-stars but from anonymous internet posters who claim to know him).
Steve Moncuse, who created the comic book Fish Police, is really unhappy with how cartoon version of it (which was made as a competitor show to The Simpsons) turned out. Moncuse had nothing to do with the cartoon other than a creator's credit, and the cartoon was very much an In Name Only adaptation. He said in one interview, "the less said about it, the better."
Charles M. Schulz felt particularly bad after the infamous "football scene" from It's Your First Kiss, Charlie Brown (where everyone continually and angrily blames Charlie Brown for his football team's loss, despite the fact that Lucy is not even trying to hide the fact that she is sabotaging him) got complaints from viewers. This is why some of the dialogue in that scene is distorted and unintelligible in later airings.
Since the 2000s, Nickelodeon has tried very hard to hide the fact that KaBlam! exists, despite its cult following and legions of former '90s babies who remember seeing the show when it was fresh and new.
Lisa Ortiz has admitted that she finds it "disturbing" that people have actually heard of Ratatoing, let alone watch it and review it.
Jon McClenahan wasn't satisfied with the end product of The Jetsons Movie, he said it was the worst animated film he had ever seen and felt embarrassed to have his name in the credits.
Joe Barbara hated the film as well due to all the Executive Meddling, and replacing Janet Waldo with pop singer Tiffany as the voice of Judy Jetson. Strangely enough, William Hanna thought the film was okay.
The casting director Andrea Romano was also dismayed by the meddling that caused Janet Waldo to be let go and replaced, and requested that her name be removed from the credits so that she would not be blamed for it.
Many of the people who worked on Pinky, Elmyra & the Brain despised working on it. In fact, just the theme song's lyrics should be enough of an indication of their disgust.
The old 15 second cartoon bumpers with The Simpsons for the Tracey Ullman Show have never been released on video or DVD, nor are they ever shown on TV. Matt Groening feels embarassed for them because it's so crudely drawn and the jokes are just simple, basic cartoony stuff.
The episode "The Principal and the Pauper" in which Skinner is proven to be someone under another name became an old shame after the episode was made. In the words of the makers themselves: "After it was finished we realized we made a mistake."
In the DVD commentary for The Simpsons Treehouse of Horror X segment "Life's A Glitch, And Then You Die", the writers express regret over including Spike Lee and Al Sharpton (who are controversial black celebrities) among the doomed celebrities in a rocket ship headed towards the Sun. They also said that someone they would have preferred to be on that ship was George Steinbrenner.
The joke in "The City of New York vs. Homer Simpson" where two people are yelling at each other in the Twin Towers in New York: "They put all the jerks in Tower One" is an Old Shame for the makers of the episode, due to the 9/11 attacks (2001).
Rather shockingly, Mike Lazzo views Space Ghost Coast To Coast, one of Adult Swim's most famous and popular shows (though Space Ghost Coast to Coast aired back when Cartoon Network didn't have an [adult swim] line-up and was nothing but wall-to-wall Hanna-Barbera cartoons, with some Warner Bros and MGM cartoons mixed in, and, later, Japanese cartoons and the "Cartoon Cartoon" in-house shows), to be this, stating that it's dead to him. This may have something to do with Seinfeld Is Unfunny (pretty much every Adult Swim show has taken at least one cue from Space Ghost; there was bound to be one that did its job better and make Space Ghost look dated in comparison).