BoJack Horseman: Despite its public and critical acclaim, many fans felt that Season 3 was unreasonably punitive of BoJack, and that he didn't deserve most of what happened to him, despite his previous actions. The Downer Ending to his plotline while everyone else's ended on a positive note didn't help. Season 4 appears to be made with this in mind; BoJack makes major strives in more positive Character Development, makes some amends with his mother, finally manages to not destroy a relationship with his half-sister Hollyhock, and several of his broken friendships are, if not mended, then at least patched up. BoJack even gets to drop the season's sole F-bomb. His own ending is an unambiguous Hope Spot, while the overall angst is about evenly divided by the Ensemble Cast, with Diane and Mr. Peanutbutter's marriage breakdown, Princess Carolyn's miscarriages and Todd's sexuality issues.
In Justice League, a three-part episode ("The Savage Time") revolves around the Justice League trying to Set Right What Once Went Wrong after Vandal Savage usurps control of the Nazis and uses them to conquer the world by way of time travel. They succeed, but the episode ends with Hitler about to be cryogenically defrosted and restored to power. This led to a massive fan-outcry, to the widespread Fridge Horror that this implied the Justice League had blithely restored the Holocaust in the process of returning to their own world. It got so bad the producers publicly stated that Vandal's manipulations meant that Hitler had neither the time nor the resources to enact the Holocaust, having been frozen before he could start and then put back in charge during the end of the Nazis' reign over Germany.
When Brainiac makes his return, he created a skullship. It's design is more closer to the comics and is meant to address complaints some people had with the other skullship that appeared in Static Shock.
During the first season, Superman had the tendency of being defeated by a number of villains frequently, sometimes in ways that wouldn't logically incapacitate him, which netted complaints. The writers caught on and the second and Unlimited seasons brought him more in line with how he was back in Superman: TAS, which resulted in him not being knocked down as easily.
SpongeBob SquarePants: Fans took issue with Mr. Krabs as a Karma Houdini for the past few seasons, but episodes such as "The Cent of Money" have him finally getting some comeuppance.
An even better example is the return of the show's creator, Stephen Hillenburg, which is explained in detail in the Animated Films folder.
The extensive Love Triangle subplot between Korra, Mako, and Asami in Book 1 of The Legend of Korra was widely panned as bring rushed, getting in the way of the real story involving the Equalists, and ultimately feeling shallow and unsatisfying. Season 4 featured a Clip Show episode with the first segment exclusively dedicated to Mako's messy love life, with side characters pointing out all the mistakes that Mako made. Mako ends up agreeing with them and admitting his mistakes, in what was basically an apology to the fans. In general, Book 3 was this after Book 2 in correcting numerous mistakes from re-railing several characters that had been become jerks, idiots and/or weak, giving a proper reason for why Korra had been secluded instead of the White Lotus messing up Aang's wishes, more compelling and coolervillains to overall getting back to the franchise's Central Theme that meant the women were rivaling the men in competence again.
In Teen Titans, Cyborg was always shown firing his sonic Arm Cannon from his right arm, until one day he used his left. Fans pointed out this apparent plot hole, and some time later, during a crucial fight, he simply converts both arms to cannons.
In "The Time Traveler's Pig" and "The Deep End", Dipper has to sacrifice his potential happiness for Mabel, causing fans to complain that she never even considers doing the same. In "Sock Opera," Bill Cipher actually uses this argument, and Mabel's treatment of him in that episode, to trick Dipper into letting Bill steal his body. When Mabel confronts "Bipper" at the end of the episode, he almost talks her into sacrificing Dipper for her own happiness...only for her to remember how often he helped her and refuse, saving the day.
The Lion King spin-off The Lion Guard's very first episode addressed the long term criticism of The Lion King promoting "segregation" of the hyenas and the portrayal of them as evil. Jasiri is the first non-antagonistic hyena introduced in the series (the second if you count book canon) and she mentions that the roles hyenas play are just as much a part of the Circle of Life as the lions. It goes so far as to retcon-away the evil nature of hyenas; apparently they are mostly good as a species, it's just The Pride Lands have coincidentally seen more evil ones than good ones.
In the first season, there was a Courtroom Episode where Kaeloo wins against Mr. Cat by emotionally manipulating him and then harshly punishes him despite him being nice to her for once. This episode was hated by nearly the entire fandom, who thought the episode was too unfair to Mr. Cat. Then, Season 3 had another Courtroom Episode, and this time around, Mr. Cat won by hoisting Kaeloo by her own petard, which the fans thought she deserved.
Episodes like "Let's Play Golf" and "Let's Play Danger Island Survivor" prove that Kaeloo is not a Karma Houdini after all, assuaging the wrath of fans who watched the episodes where Kaeloo does get away with some pretty shitty stuff.
Fans of the series who felt like Mr. Cat and Stumpy got too much screen time were pretty happy with Episode 149, where Mr. Cat does not appearnote For the first time in the series and Stumpy is relegated to a minor/supporting character while Kaeloo and the bunny twins get more focus.
Many fans of the show felt annoyed by Kaeloo's constant manipulation of Mr. Cat's emotions and her using his love for her against him. In Episode 108, we get to see her emotional blackmail backfire on her while Mr. Cat watches with a confident smirk.
The Simpsons episode "Brother, Can You Spare Two Dimes?" was hastily developed and tacked onto the end of Season 3 after the negative response to the Downer Ending of Season 2's "Oh Brother, Where Art Thou?", and specifically overrides said Downer Ending, with Herb regaining his fortune and reconciling with Homer.