One possible scenario could be a misunderstanding. Maybe Molly misinterprets Hermione's actions regarding Ron. For example, if Hermione is being strict with Ron about his studies or his behavior in the fanfiction, Molly, being Ron's mother, might take it the wrong way and say something harsh to Hermione, thus hurting her. Another situation could be related to Hermione's Muggle - born status. If in the fanfiction, there are some rising tensions about pure - blood and Muggle - born wizards, Molly, who is from an old wizarding family, might accidentally let her old - fashioned views slip and make a comment that offends Hermione.
In some fanfictions, it could be about Hermione's relationship with Harry. If Molly has certain expectations about Harry's future and Hermione's influence on him doesn't align with those expectations, she might lash out at Hermione. For instance, if she thinks Hermione is leading Harry into dangerous or unapproved paths, she could say things that wound Hermione's feelings. Also, if there are family secrets or traditions in the Weasley family that Hermione unknowingly steps on, Molly might get angry and hurt Hermione in the process.
One scenario could be when Molly tries to interfere in Hermione's relationship with Ron. Hermione might stand up and say that she and Ron will figure things out on their own terms, not according to Molly's old - fashioned ideas. For example, if Molly tries to push for a quick wedding, Hermione could firmly state that they are focused on their careers and personal growth first.
One possible reason could be jealousy. Maybe Molly is jealous of Hermione's intelligence and the special bond she has with Harry and Ron. Another reason might be that she feels Hermione is a bad influence on her sons in some way. For example, she might think Hermione's Muggle - born status could bring trouble to the family in the wizarding world which is full of pure - blood supremacist ideas.
Well, sometimes in fanfiction, authors like to explore dark and twisted ideas. Maybe they want to create a contrast to the kind Molly Weasley in the original series. It could be a way to add drama and conflict to the story, even if it's a bit out of character for the Molly we know.
It could create a rift in the friendship between Hermione and the Weasley family. If Hermione is hurt, she might distance herself from them. This would be a big change as the Weasley family has been like a second family to Hermione. It would also affect Ron, who is in love with Hermione. He would be caught in the middle between his mother and Hermione, which could add a lot of drama to the story.
Some Hermione fans might be outraged. They love Hermione and seeing her hurt in such a way, especially by a character like Molly who is supposed to be good, could make them very angry at the writer.
Molly could have made some inappropriate comments about Hermione's blood status. Even though Hermione is a Muggle - born, she has proven herself time and time again in the wizarding world. If Molly makes a snide remark about her blood, Hermione would surely tell her off for her prejudice.
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.
One scenario could be that Hermione is being bullied by some pure - blood supremacists at Hogwarts for being a Muggle - born. Mrs Weasley, who has always been inclusive, finds Hermione crying in the library. She sits down with her, hugs her tightly, and tells her that her blood status doesn't define her worth. Mrs Weasley might also offer to teach Hermione some of the Weasley family's special spells to make her feel more confident.
Perhaps Hermione confronts Ron about his lack of commitment to their friendship or to their studies. In the fanfiction, she might be tired of always having to push him to do better and finally snaps at him. For example, she could bring up all the times he's slacked off during group projects or when they were preparing for exams.
Harry would also be very protective of Hermione. He would likely step in between Molly and Hermione, using his status as the Boy Who Lived if necessary to defuse the situation. He might try to reason with Molly, reminding her of all the good things Hermione has done for them and for the wizarding world.