If in the fanfiction Scott starts to change in a way that Stiles doesn't like. For example, if he becomes more power - hungry and is willing to sacrifice their friendship for power. Stiles, who values their friendship and has a strong sense of right and wrong, would hate Scott for such a transformation. This would also create a lot of emotional turmoil and interesting plotlines in the fanfiction.
Perhaps in the fanfiction, Scott falls in love with someone that Stiles also has feelings for. This love triangle situation could turn Stiles' feelings into hatred as he sees Scott as a rival for the person he cares about. Also, if Scott accidentally reveals one of Stiles' secrets that he promised to keep, Stiles would likely be very angry and could start to hate Scott.
In some fanfictions, Scott might betray Stiles by choosing the wrong side in a conflict. For example, if there's a power struggle between different supernatural groups, Scott could side with a group that has intentions harmful to Stiles or his family.
One possible scenario could be that Derek wants to gain Scott's trust. Since Stiles is Scott's best friend, Derek might think that by getting closer to Stiles, he can have an in - road to Scott. For example, he could ask Stiles to pass on messages to Scott or arrange meetings through Stiles.
One possible scenario is that Minato was resurrected in a wrong way in the fanfiction. His behavior after resurrection was not what Naruto expected. Maybe he was more cold - hearted or seemed to have different priorities that didn't include Naruto, so Naruto started to hate him.
It could be that Percy gets involved in a conflict where he sides against Artemis' hunters. His actions in this conflict might make Artemis view him as an enemy. For example, if he accidentally harms one of her hunters while trying to protect someone else, she may grow to hate him.
Perhaps in the fanfiction, Sirius gets involved with the wrong crowd. And Harry, who has a strong sense of right and wrong, can't stand being associated with Sirius any longer. Or maybe Sirius has a falling out with one of Harry's other important people, like Hermione or Ron, and Harry takes their side and starts to hate Sirius as a result.
One possible scenario is if Naruto is constantly blamed for the team's failures. For example, if every mission that goes wrong is pinned on Naruto, even when it's not his fault, he might start to hate the team. This could be due to a misperception by the other members or a malicious plot within the fanfiction world.
One scenario could be that Edward accidentally endangers Bella's family in the fanfiction. Since Bella is very protective of her family, this could be a major turning point for her feelings towards him. For instance, if his vampire nature attracts some dangerous vampires to Forks and they target her family.
One possible scenario is that Jacob reveals a secret that Bella doesn't like. This could make her feel betrayed and start to hate him.
One possible scenario is when the imprint causes Jacob to be very protective of the person he imprints on. Bella might see this as Jacob neglecting their previous friendship or bond. Another scenario could be that the person Jacob imprints on has a negative attitude towards Bella, and Jacob seems to side with the imprinted one, making Bella hate the whole situation.
In the fanfiction, it might cause Stiles to question his trust in Scott. Their relationship could become strained as Stiles distances himself from Scott. Scott, on the other hand, would be desperate to regain Stiles' trust. He might go to great lengths, such as seeking advice from other friends or taking on extra risks to prove his loyalty to Stiles.