In some fanfictions, there could be a power struggle between Bella and Jacob. Maybe Bella wants to have more control over her own life and decisions, but Jacob keeps trying to impose his will on her. This could lead to a lot of tension and ultimately result in Bella hating Jacob. Also, if there are differences in their beliefs or values in the fanfiction, like Jacob believing in a certain way of life for werewolves that Bella completely disagrees with, it could cause animosity.
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.
Another scenario could be that Bella does something that endangers Jacob's family or the werewolf pack. This would make Jacob see her as a liability and develop hatred towards her. In some fanfictions, she might accidentally expose the werewolves to their enemies because of her association with the vampires.
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.
Sure, in certain fanfictions Bella ends up with Jacob. Sometimes, the fanfic writers rewrite the whole Twilight plot, making Jacob a more appealing character for Bella from the start. They might have Bella and Jacob meet under different circumstances that lead to a stronger bond between them right away. It could be something like Jacob saving Bella in a different way that makes her see him in a new light, and as the story progresses, their relationship blossoms into a romantic one.
In some fanfictions, they might kiss after a long period of misunderstanding. Jacob has been misinterpreting Bella's actions and vice versa. But when the truth finally comes out, they kiss as a way of sealing their new - found understanding and connection.
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.
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 reason could be that some fans want to explore a different dynamic. In the original story, Edward and Bella are in love, but in this fanfiction, perhaps the writer wants to show a more complex relationship where Edward hates Bella. Maybe it's to add more drama or to explore an alternative storyline that goes against the typical romance.