The first, Tintin in the Land of the Soviets (1929), is ripped off wholesale from a single book condemning the Communist regime and has extremely primitive art, which was never updated. Hergé only republished it during the 1970s and solely because to many bootleg copies were sold. Still, it was kept in its original black-and-white form, without any alterations, and in an act of Canon Discontinuity kept out of the regular Tintin canon.
The second, Tintin in the Congo, is considerably racist, even for its time, in its caricatured drawing of African characters and depiction of them as lazy and childlike, causing a furor in the UK when it was reprinted. There was also an unsuccessful private prosecution in Belgium to try to get the book banned as incitement to racism. Tintin's psychotic maiming of wildlife (blowing up a rhinoceros with a drilled hole and a stick of dynamite) is pretty hard to take as well. Hergé recognized this in retrospect and begged for them to be left out of print. Unlike the Soviet adventure, Tintin in The Congo was later redrawn and republished in color and with Hergé's later more polished art style. The rhinoceros was spared in the Scandinavian edition (except for the newest Swedish translation) and the English color edition.
A third example is Shooting Star, created during the Nazi occupation of Belgium; it originally featured stereotyped Jewish-American villains who in later versions were altered to be of unindicated ethnicity. A very antisemitic scene with two rabbis was left out of the story.
Quick and Flupke: Some episodes in which Quick and Flupke playfully imitate Hitler and Mussolini were never reprinted. During the 1930s it was just meant as an innocent joke, but after World War II these gags were suddenly not that funny anymore.
The 1930s Mickey Mouse comics count as this, since many of them contain racist stereotypes, Mickey attempting suicide, and other themes contrary to the image of Mickey Mouse today. Because the comics themselves were believed to be in the public domain, Eternity Comics, an independent company not affiliated with Disney, attempted to anthologize "The Uncensored Mouse" in comic-book format in 1989 without permission from Disney, doing everything they could to prevent a lawsuit (using all-black covers, shrink-wrapping them so nobody would flip through the books, acknowledging Disney's rights in the copyright page, etc.). They were shut down anyway, because even if the comics were in the public domain (which is questionable), the characters weren't.
Jhonen Vasquez, author of Johnny the Homicidal Maniac, Squee, and creator/showrunner of Invader Zim put out a single-issue "throwaway" comic called the Bad Art Collection early in his career, which was exactly what it says on the cover. When someone brought a copy to a signing event at a convention he responded with his usual good grace and humour; and commented, laughingly, "Oh my God, someone actually bought this thing," while signing it. According to Vasquez, the origin of the collection was him writing the cartoons back in school in order to get people to stop bugging him to draw for them. Unsurprisingly, the Bad Art Collection has been out of print for at least a decade.
Mexican cartoonist Rius published many comic books in the 60-70s. Being a firm believer in Marxism, he dedicated much of his work to socialism/communism and prophesized the fall of capitalism. One of the most famous examples of this is the book he made under orders of the Cuban government about the Cuban Revolution. After the fall of the Berlin Wall and the collapse of the Soviet Union, he admitted that he had to eat his own words and that he never drew anything negative about the socialist states of the time because, in his own words, he "didn't want to provide ammunition for Imperialism."
While they don't regret writing Amethyst, Princess of Gemworld, creators Dan Mishkin and Gary Cohn wince in hindsight at their inclusion of Attempted Rape early in the series, and Cohn says it'd be the first thing to go if he ever had another go at it.
Despite this, the short-lived New 52 version of the comic (by Jem and the Holograms creator Christy Marx) also included an attempted rape scene.
Robert Kirkman introduced the character of Freedom Ring during his run on Marvel Team-Up, a gay hero who was touted by Joe Quesada himself as an upstanding example of gay male characters in the Marvel Universe... who was then killed horribly at the end of the three-issue arc. Kirkman apologized for "killing 25% of Marvel's gay population," admitting that he wanted to write a story about a newbie hero making newbie mistakes and dying because of it, while also wanting to write a story about a gay hero, and the two plots intersected in the worst way possible.
And he very much regrets the early death of Shane in The Walking Dead. He never dreamed that the series would last as long as it has, and thinks he could have done a lot more with the character.
Marvel writer Mark Gruenwald originally created the Scourge of the Underworld as a plot device for disposing of villains who were too minor, redundant, or ill-conceived. He eventually conceded that he often expressed some disappointment in what he saw as the short-sightedness in killing so many potentially "fun" villains rather than re-imagining or improving them.
All except for Turner D. Century. He was an embarrassment to everyone at Marvel. He was created by veteran Marvel writer J.M. DeMatteis, probably in an attempt to create a creepy/surreal/absurd/insane villain with maybe a pinch of social commentary, but instead, he got one of the biggest joke villains in Marvel's history. Even DeMatteis didn't regret what happened to him.
Suske en Wiske: Creator Willy Vandersteen already made comics during the Second World War before he struck gold with Suske & Wiske after the liberation of Belgium. One of the stories he drew were antisemitic cartoons for a Nazi SS magazine. Vandersteen was smart enough to do this under a pseudonym and this Secret Shame was only revealed in 2010, literally 20 years after his death. Even his relatives claimed he never told them anything about this.
Astérix: Creator Albert Uderzo has apologized about the very anti-German "Asterix and the Goths" album. In this story the Goths (Germans) are depicted as being evil and militaristic. He said the story was made just two decades after World War II and anti-German sentiments were still vivid then. In later "Asterix" stories Germans are depicted more sympathetically.