She could be rejecting Harry's proposal because she's still dealing with past traumas or unresolved issues. For example, she might be worried about how the public would view their relationship, especially given Harry's status as 'the boy who lived'. She also might not be ready for such a big commitment due to the instability in the wizarding world at that time. There could be a lot of political and social unrest, and she might feel that getting engaged is not a priority in such a situation.
One possible reason could be that Hermione has a different romantic vision. In the original series, she might see Harry more as a friend. In the fanfic, her character could be written as being focused on her own personal growth and goals, which don't align with a romantic relationship with Harry.
One possible reason could be that Hermione sees Harry more as a friend. She has a deep, platonic bond with him and doesn't want to risk ruining that friendship by turning it into a romantic relationship. In the original story, they have been through so much together as comrades in the fight against Voldemort, and she may value that camaraderie above all else.
It could also be due to a series of unlucky events. Suppose Hermione's well - intentioned plans keep backfiring in a way that makes Harry question her judgment. Like when she tries to solve a problem but ends up making it worse, Harry might start to lose trust.
Perhaps he tries to convince her. Harry is a determined person. He might think that Hermione just needs more time or that he didn't present his case well enough. So, he could start listing all the reasons why they would be good together, from their shared history to their mutual understanding of the wizarding world. But if Hermione remains firm in her decision, he may finally have to accept the rejection and move on.
Another reason could be a rift in their friendship caused by outside factors. For instance, if the wizarding community starts to turn against Harry because of false rumors or misinformation, Hermione might find it too difficult to stand by him. She may fear for her own reputation or safety, and this could lead to her abandoning Harry.
In the fanfic, it might be due to some sort of magic gone wrong. There could be a spell that made her act out of character. It's not unheard of in the wizarding world for spells to have unexpected effects on a person's behavior and relationships.
One possible reason could be if Harry takes a big risk without consulting her first. In the wizarding world, their adventures are full of danger, and Hermione is often the cautious one. If Harry jumps into a situation like facing a powerful dark wizard alone without a proper plan, Hermione would likely blame him for being reckless.
In fanfics, the relationships between characters can be explored in new ways. If the fanfic writer decides to show a rift between Hermione and Harry for the sake of drama, they might create situations where Hermione doesn't believe Harry. This could be due to a series of miscommunications or actions that Harry takes which seem out of character to Hermione.
One possible reason is that the fanfic writer wants to create conflict. By making Hermione not believe Harry, it adds tension to the story.
Perhaps Harry was seen spending a lot of time with a new character, a girl who was really good at magic and Hermione suspected that Harry was getting some sort of unfair help from her in terms of academics. It could also be that there were some rumors going around in Hogwarts about Harry having an unfair advantage, and Hermione, being the stickler for rules and fairness, immediately jumped to the conclusion of cheating.