Thanks to Alain beating Ash in the Kalos League, many viewed his inaction as Ash was captured by Team Flare as outright betraying him to them◊. In context, Alain was unaware of their villainy until then and was then too stunned by their actions and his own guilt to act. Subsequent fan art outright invented flaws, like stealing Serena despite being even less romantically inclined than Ash. Despite his massiveMy God, What Have I Done? over his actions, several people still think he should have been stripped of his status as Kalos League champion, despite earning it fairly and it being the one of the few things he did not connected to Team Flare.
Speaking of which, one of Ash's other league rivals, Tobias, due to his status as his most disliked "rival introduced in league conference that beats him" thanks to barely being alluded to and using a Legendary (Latios) and Mythical (Darkrai) Pokemon, it's rare for fans to put him in a positive light. At best, he's an asshole that overly relies on said Olympus Mons, otherwise he's a total rookie, at worst, a power-hungry, legend seeking villain who's willing to kill others just to obtain another legendary into his collection. This is in stark contrast to his canon counterpart, who is a good sport and compliments Ash on putting up as much of a fight as he did.
While some of Iris' actions have understandable reasons to be criticized by some fans, some fans exaggerate the things she did that they didn't like while purposefully ignoring good things she did.
Some fanfics tend to portray Serena as a full-on Yandere towards Ash, especially if the fic in question features a pairing between Ash and a different one of his female companions. Other people who dislike Serena tend to exaggerate her personality by calling her a bitch and a slut (when really, she's a nice person in canon) and want her murdered simply for being on the show.
Infinity Train: Blossoming Trail has an In-Universe example with Chloe painting Ash, Goh and Professor Cerise in this light when talking about them to other characters on the train. While this makes sense considering her rocky relationship with her best friend and her dad (Goh started neglecting their friendship because of his Mew obsession, while the professor is too caught up in his Pokémon research to bond with his daughter), Ash is only this because he's well-liked and manages to easily get the other two's attention thanks to a shared love of Pokémon that Chloe lacks. This is even reflected in the narrative, as her number rises when she tries to convince herself that this grudge goes both ways and Ash has no interest in her, when he has actually tried multiple times to befriend her.
As of Arc 2, Parker sees both Goh and Ash as this in story as well, especially the former for leaving his sister behind for Mew. As for Ash, Parker is angry that Ash didn't even try to connect with his sister, never considering that Chloe made about as much effort to connect with him, if not even less considering Ash at least invited Chloe to do things with them.
A sub-section of commentary in story is about Professor Cerise favoring Goh and Ash over his children. This interpretation relies heavily on the idea that nothing happens offscreen, ignores the fact that Ash and Goh work for him so you might as well argue the same thing about Renji and Chryssa, hypes up what he and Ash do come off like when interaction as far more casual and friendly than it actually is in canon, and basically serves as an additional means of justifying Chloe and Parker's actions while demonizing them.
Delia Ketchum doesn't like Chloe Cerise. The reasons are fairly understandable in the text: Delia's seen how Chloe's (in)actions have made those around her miserable, up to and including her son having nightmares so bad she thinks he's about to have a seizure. To some readers, Delia spends all her time ranting and raving about Chloe and how she deserves death, when in reality Delia has many scenes where Chloe rarely comes up, if at all, and they ignore her legitimate reasons to not want the girl in her life.
Because of Goh's Base-Breaking Character status, many fans have taken to characterizing him as a Pokemon Hunter, a thief of Mons which "rightfully" belong to Ash, an abuser that would make Paulunnerved, or even abusive to Ash and Chloe. After he ended up capturing the Grookey that had originally belonged to Team Rocket, it got particularly bad as fans on both sides, but particularly Japan, begun calling him a thief in serious discussions. This had gotten so bad that Bulbagarden Forums had to post a PSA about not calling him a psychopath.
Ash's father. The vast majority of the time that he comes in the base series, he is not spoken of in the negative. Delia spoke of him positively in the second episode, and two of the three times he came up in the continuity started by Pokémon: I Choose You! the discussion is entirely positive (the third time was Delia complaining that he and Ash don't call her enough in the titular film). However many fans, especially in the west, tend to write him as a deadbeat or a villain, often Giovanni, his absence being treated as abandonment of both Ash and Delia. This is a case of differing values between Japan, where the work culture has many fathers be away for long periods of time to support their families without it being seen as wrong, and the West, where families are expected to be in frequent contact with each other. While the idea of Ash's father being a deadbeat is not unheard of in Japan (see Pocket Monsters: The Animation), it is much more common in western discourse than Japanese discourse.
Erika tends to get this thanks to a case of Common Knowledge (fans misremember that she never banned Ash from her gym in the English dub, only her store; her assistants were the ones who kept him from entering the gym, and Erika later points out she's supposed to accept all challengers). Fans tend to exaggerate her negative traits, ranging from having her refuse to challenge anyone who dislikes her perfume to making her an out-an-out misandrist/Psycho Lesbian.
Games
Lusamine is an interesting example, where not only are there those who hate Lusamine and don't believe that she can be redeemed, but fans of the character also tend to double-down on her being an Abusive Parent, tone down her Tragic Villain nature, and dismiss any adaptations that ditch the abusive mother angle (i.e. USUM and the anime) or have Lusamine herself question if she deserves her childrens' forgiveness (Masters).
While he's clearly meant to be seen as a loving, but overprotective worrywart, Bianca's dad from Pokémon Black and White is often written to be a violent abuser in fanfiction. Kynim's Pokemon White Nuzlocke comic is a famous example, where he's not merely abusive, but a stereotypical sexist southerner as well.
Kamado from Pokémon Legends: Arceus is a Well-Intentioned Extremist at his worst; everything that he does — even exiling the Player Character out of a mistaken belief that they're behind the time-space rifts — is done to protect his settlement. Some fans, largely those who don't forgive him for exiling the player, tend to exaggerate him into a ruthless dictator who repeatedly tortures the player character for being an outsider.
For all of Professor Sada/Turo's negative qualities, it is confirmed that they truly did love their son, his dog and the Legendary dragon (having started their "paradise" for the former and sacrificed their life for the latter) and had noble intentions (or at least what they thought were noble intentions) beneath their plans. The fandom would have you believe that they were unrepentant sociopaths who remorselessly murdered their entire research team to achieve their goals (something that is never stated anywhere in the game) and didn't care about their son at all.
Kieran's detractors often paint him as a Yandere who could actively become murderous if his desire to have Ogerpon/defeat you wasn't sated, an outright incel who treats Ogerpon as a shiny prize to be won (ignoring the facts that 1. Kieran is a child and 2. his idealized view of Ogerpon is closer to Loving a Shadow than seeing it as an object), or just a plain vanilla Spoiled Brat who needs to get over himself (ignoring that the game shows multiple times that Kieran was pushed to this point by outside sources on top of his already existent issues, and that the protagonist and Carmine are both just as at fault for how he turned out as he is).
Carmine gets a bit of this too. Some have taken the "I WAS being kind! It's not like I hit him or anything!" comment to imply that Carmine has inflicted physical violence on Kieran (which, while not impossible, is never outright stated and the wording could just as easily mean that Carmine is just Comically Missing the Point), or twisted her dislike of people not from Kitakami visiting the region into outright racism (ignoring the explanation she gives at the end about how her reasoning was that she feared they would reduce the homeland and culture she loves into a kitschy tourist attraction, a sadly very real concern for a lot of cultures in the real world). There's also a tendency to pin the blame for Kieran's descent into villainy solely on her, despite the fact that, while she is part of it, the player character and Kieran's own emotional and psychological issues also contributed to the situation.
The player character occasionally gets this from players who give Kieran the Draco in Leather Pants treatment. They're treated as being completely responsible for Kieran's Sanity Slippage, ignoring the fact that the game never gives you the chance to do anything else, Carmine's communication issues also didn't help, and Kieran already had some of his own issues to begin with.
In-game, Drayton's Manipulative Bastard tendencies only came out from his desire to help Kieran and the League Club. If you asked the fandom (especially Kieran fans), they'd say that he did it either for Revenge or For the Evulz. While the revenge angle is implied to be a motivation of his post-Mochi Mayhem, he mentions it in a more playful manner than malicious one (not that Kieran isn't still upset, since he won't stop bringing it up), and some of Drayton's more ardent critics tend to flatten it to his only motivation.
The old couple who took in Pecharunt in its backstory have been called "abusive" towards it for making constant demands that eventually led to it traveling to Kitakami with the Loyal Three to take Ogerpon's masks (which in turn led to the deaths of Ogerpon's old trainer and the Loyal Three, Ogerpon being shunned and Pecharunt itself being forced into hiding). This ignores the fact that they only made those demands because Pecharunt itself craved the love they were already giving it so much that it fed them poisonous mochi that brainwashed them and exacerbated their greed. And this is all without mentioning the very real possibility that this account isn't as reliable as it's presented as being.
◊. In context, Alain was unaware of their villainy until then and was then too stunned by their actions and his own guilt to act. Subsequent fan art outright invented flaws, like stealing Serena despite being even less romantically inclined than Ash. Despite his massive My God, What Have I Done? over his actions, several people still think he should have been stripped of his status as Kalos League champion, despite earning it fairly and it being the one of the few things he did not connected to Team Flare.
