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.
She might give him cold stares in class. Hermione is not one to shy away from showing her emotions through her expressions. So, every time Snape is in her line of sight, she could fix him with a withering glare that clearly shows her displeasure.
One possible reason could be that Snape sees Hermione's value as a brilliant student. He might recognize her potential and not want it to be wasted just because of her dad's actions or situation. Maybe he has a sense of justice deep down, despite his often cold exterior.
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 reason could be differences in teaching methods. Hermione is a very studious and by - the - book student, and Snape has his own rather unorthodox and often harsh teaching ways. For example, in the official books, Snape is known for his sarcastic remarks towards students, and Hermione might not tolerate this in a fanfiction scenario. She could argue with him about how his teaching is not conducive to a positive learning environment.
One reason could be Hermione's intelligence. Snape might recognize that she is smart enough to understand his complex situation. He could see her as someone who could offer a different perspective on his problems.
One possible reason could be a misunderstanding. Maybe Hermione thought Snape was involved in some dark plot against her friends. In the wizarding world, there are often secrets and deceptions, and if she got some false information, it could lead her to take such drastic action.
Hermione could be hiding her pregnancy from Snape because she's not sure of his feelings towards her. There may be an ambiguous relationship between them. She might be in love with him, but not sure if he feels the same. And she doesn't want to burden him or make things awkward between them. Or perhaps she suspects that Snape might be involved in something dangerous, and she doesn't want her unborn child to be dragged into it.
One possible reason could be Snape's unfair treatment of Gryffindor students. Hermione, being a strong advocate for justice, might not tolerate his constant jabs at her house. For example, in the original story, Snape often took points from Gryffindor without what Hermione might consider proper cause. In fanfiction, this could be exaggerated, leading to her blowing up at him.
Perhaps she's being bullied. In the wizarding world, there could be other students who pick on her because she's a 'Mudblood'. This could be really distressing for Hermione, and when Snape finds her crying, he might be conflicted between his general dislike for Gryffindors and his sense of justice.
Perhaps he discovers some secrets about his parents that he doesn't like. For example, he might find out that they were involved in some dangerous or unethical magic before. This new knowledge could make him angry at them for putting themselves and their family in jeopardy.