One possible reason could be that Hermione might be too overbearing in her studies and constantly nags Harry about his schoolwork in the fanfiction. This could annoy Harry and make him mad.
Maybe in the fanfiction, Hermione makes a decision without consulting Harry, something really important like a plan to deal with a dark wizard threat. Harry might feel left out and angry because of that. For example, if she teams up with other characters and leaves Harry in the dark, it would surely make him mad at her.
One possible reason could be a misunderstanding. Maybe there was a miscommunication about something important, like a plan to fight against the Dark Arts. For example, if the Weasleys accidentally left Hermione out of a crucial part of the plan, she might be very angry.
One possible reason could be that he's worried about Ginny's safety during the pregnancy. He might be overprotective and his concern comes out as anger.
Maybe Snape made a snide comment about Hermione's intelligence or her Muggle - born status. Snape has a rather acerbic tongue, and if he said something derogatory about Hermione's abilities or her heritage, she would surely be furious. After all, Hermione works extremely hard to prove herself in the wizarding world and any attack on her intelligence or background would be a big blow.
It could be due to jealousy. Perhaps Ginny has been spending a lot of time with another character, and Harry misinterprets their relationship, leading to his anger. In fanfiction, the writers often play with such emotions to create drama.
Maybe Dumbledore made a decision that put Harry in great danger without his knowledge. For example, sending him on a dangerous mission without proper preparation.
One possible reason could be that the writers lost interest in the Harry Potter fandom. Maybe they found other fandoms or stories more appealing.
In some fanfictions, there might be a new magical element or prophecy that makes Harry question Hermione's motives. If the prophecy says something about Hermione being involved in a dark plot, even if it's false, Harry may start to have doubts about her.
In fanfiction, Hermione's obsession with Harry could stem from her own insecurities. She may see Harry as someone who is more confident and free - spirited. She is obsessed with him as she wants to be part of his world, which seems more exciting compared to her own studious and rule - following nature. Additionally, their friendship has a strong foundation, and the writers of fanfiction might exaggerate this into an obsession to explore different storylines.
Maybe it's about her study habits. For example, she always preaches about everyone following the rules in class and doing their homework properly. But then she might break a minor rule herself when it comes to getting access to a certain book in the library for her research.
It goes against the canon. In the original 'Harry Potter' books, their relationship is clearly a deep friendship. Changing it to a sexual relationship in fanfiction is a misrepresentation.