In the episode "Challenge of the Samurai", Ash Ketchum spends much of the episode being berated by the titular character for not finishing what he started (not stopping a Weedle from escaping, thus letting it summon a swarm of Beedrill). However, the only reason the Weedle escaped was because the Samurai surprised him as he was about to capture it, because he didn't have the courtesy to wait until Ash was done catching it. Yet Ash is meant to accept responsibility for what went wrong, even though nothing was his fault, and though he defeats the Samurai, he's still short one Weedle which would someday evolve into a Beedrill. All of this is duly mocked in the Pokemopolis review of the episode.
In the episode "Pokémon Scent-sation!", the gang visits a perfume boutique in Celadon City. Ash comments that he doesn't like the smell of perfume. This results in him getting kicked out of the store by the manager. Simple enough, but then when Ash tries to challenge the gym in Celadon City, it turns out the Gym Leader is the same manager from the shop and she bans him from entering the gym. Naturally, this is all Played for Laughs, but the episode wants to portray Ash as being the stubborn one.
Part of the premise of Delicious in Dungeon with the In-Universe taboo against eating monsters. Wanting to avoid eating humanoid monsters is understandable thanks to Carnivore Confusion but eating those that are animal type is wrong because...it just is. Even though most of them are safe to eat and many of them are essentially just bigger, more beastly versions of normal animals. Most characters encountered balk at the idea of using monsters as food despite how much easier it makes Dungeon Crawling thanks to relieving adventurers of the burden of buying and carrying large amounts of supplies. There are adventurers who do it (someone had to write Laios's guidebook after all) but it still seems to be an interest that's niche at best and reviled at worst.
In WORKING!!, Souta is repeatedly made the bad guy for complaining when Inami punches him. Except, you know, she's punching him, with super-strength, and whenever she gets close, for no reason other than her illness. To be fair, he does get kinda rude sometimes, but it's hard not to sympathize with his plight.
Knuckles would frequently fall victim to this. While he was usually the most serious and vehement on getting the job done, the others were more than willing to turn everything into a game. He would often question the ethics of a plan the team made, only to be bullied into following it through. Most times the plan would fall apart, but he would never call them out nor would the team be remotely apologetic for ignoring him. In one case the team outright steal the Master Emerald from him for their mission (keeping in mind the established importance of the emerald to Angel Island). When Knuckles is rightfully angered by this, the team label him selfish and inconsiderate and outright beat him up.
Vector gets taken to task for suggest Cream, a six-year-old girl, should be sent home to her mother Vanilla instead of sticking around with Sonic and friends. They all call Vector heartless because Cream wants to stay, but whether she wants to stay or not shouldn't factor in. Cream is a huge liability for Sonic and crew; she is, at best, The Heart of the team, and otherwise not useful to their mission. Even assuming she'll be looked after by the Thorndykes' staff, Sonic is fighting off monsters and threats to the planet, meaning Cream isn't safe anywhere on Earth! It also doesn't help that Cream's age makes her an easy target for kidnappings. While Vector is portrayed as sticking his nose where it doesn't belong, there's really no reason for Cream to stay.
After the Saiyan Saga in Dragon Ball Z, after the Saiyans are defeated (in the anime version at least), when Gohan announces he wants to go to Namek, Chi-Chi gets upset and scolds Gohan about how she wants him to act his age, and she talks about how she didn't see him for a whole year. The show obviously expected fans to side to side with Goku/Gohan's point of view on what's important so it would make Chi-Chi look much worse than she really is, ignoring the fact that Chi-Chi had a valid point. Had Gohan been an older teenager or an adult, this would be justified.
In Dragonball GT, when Bulma is called out for discovering the Dragonball when she was 16, she blames Goku for it. The writers expect us to side against Bulma for indirectly causing Omega Shenron to appear, and expect fans to ignore the fact that Bulma did not intend for Omega Shenron to show up and it was all a complete accident in her case.