Another reason could be related to school work. If there are new rules in Hogwarts that she deems unfair regarding academics, like restrictions on library access or new grading systems that don't reward hard work properly. Hermione is all about learning and fairness in education, so this could really make her angry.
A major reason could be differences in their approaches to fighting the dark forces. Maybe in the fanfic, Hermione wants to use a more diplomatic and academic approach, Ron is hesitant and just wants to follow the status quo, and Harry wants a more direct and action - based approach. Their inability to reconcile these differences can lead to Harry being angry. For example, when they are planning how to deal with a new dark wizard threat, their arguments and lack of compromise can make Harry frustrated and angry with them.
One common reason is Hermione's over - protectiveness. Sometimes she tries to control situations too much, which can make Harry feel suffocated and thus angry. For example, in some fanfictions, she might try to stop Harry from taking risks in a dangerous mission, which he sees as her not believing in his abilities.
In some fanfictions, Harry might be angry with Ron and Hermione if he feels they are keeping secrets from him. For example, if they discover something important about Voldemort's plans but don't share it right away, Harry could get angry. He's used to relying on them and when that trust is broken, even if it's a misunderstanding, his anger can flare up.
One possible reason could be misrepresentation of her character. In some fanfictions, authors might change her personality to fit a certain plot, like making her overly jealous or mean, which would be out of character for the gentle Hinata. This could make her seem unlikable and thus anger fans who love the original Hinata.
One possible reason could be that Tsunade makes a decision regarding the village that Naruto strongly disagrees with. For example, if she refuses to send help to a neighboring village in need, Naruto, with his strong sense of justice, might get angry. He's always been about protecting and helping others.
One reason could be Boruto's recklessness. In fanfiction, Boruto might engage in dangerous stunts or actions that go against Naruto's teachings. For example, if Boruto were to use a forbidden jutsu without fully understanding the consequences, Naruto would be angry as it not only endangers Boruto but also those around him.
In a fanfiction, Natsu might get angry if he was wrongly accused of something. Say, if he was blamed for a crime he didn't commit in the guild or in the magical world at large. He's an honest person, and being falsely accused would be a huge blow to his pride. Another possible reason is if a magic - based experiment went wrong because of someone else's carelessness and it put his friends in danger. Natsu values the safety of his comrades, and such a situation would make his blood boil. Also, if someone were to try and break up the Fairy Tail guild by causing internal disputes, Natsu would be enraged as he loves the unity and spirit of the guild.
One possible reason could be jealousy. Maybe Jackson has something Stiles wants, like popularity or a girl he likes. For example, if they both like Lydia, Stiles might get angry at Jackson's smooth ways with her.
In the fanfiction, it could be that Kakashi is being too hard on Naruto during training. He might be pushing him beyond his limits without proper explanation or support, causing Naruto to feel frustrated and angry. Naruto is a determined character, but everyone has their breaking point.
It could also be that Hermione has a sense of propriety about the stories of her world. Fanfiction might distort or misinterpret events and characters in ways she doesn't like. For example, if a fanfiction portrays her friends in a negative or inaccurate light, she would likely stay away from it. And she may have a loyalty to the original stories and authors, and view fanfiction as a bit of a violation of that.