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.
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.
She might hate it because it could change the way people see her character. In the original story, she is a strong and independent person, but fanfiction might portray her in a wrong way.
She might be hurt at first. Since she's pregnant, her emotions could be more fragile, and Harry's anger could really sting.
It could be that Harry made a decision that went against Molly's values. Suppose Harry started using dark magic or got involved with some unsavory characters, Molly, being a morally upright witch, would be furious with him. She might feel that he is setting a bad example for her kids or bringing danger to their world.
Often, it starts with the initial moment of Harry getting mad. Then Ginny tries to figure out why he's so angry. For example, she might approach him and ask directly, but Harry could be too stubborn to tell her right away.
In some fanfictions, Ginny might be mad at Harry because of a misunderstanding. For example, she could misinterpret his actions towards another girl as being unfaithful. Maybe he spends a lot of time with Hermione on a project and Ginny thinks there's something more between them.
In some fanfictions, Ginny might be written to betray Harry because of a prophecy. The prophecy could mislead her into thinking that Harry was going to bring doom, and so she decides to act against him to prevent that. It's a different way of looking at their relationship compared to the original story, where their bond was based on love and trust.
One scenario could be that Harry Potter accidentally breaks a family heirloom of the Weasley family while at the Burrow. Molly, who treasures her family's possessions, would be very angry with him. Another possibility is that Harry gets into a fight with one of her sons, like Ron, and Molly takes her son's side, getting mad at Harry for starting the argument.
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.
It might be that there was some sort of misunderstanding. For example, a rumor spread that Harry was getting too close to one of his female colleagues at work. Ginny, being a fiery character, got mad without really knowing the truth. In fanfic, these kinds of misunderstandings are often used to create drama.