In a fanfiction, it could be that Ginny is being too reckless. Hermione, being the more cautious one, is always worried about getting into trouble. If Ginny is constantly sneaking out or getting involved in dangerous adventures, Hermione might yell at her to stop putting herself and others at risk.
One possible reason could be jealousy. Maybe Ginny is jealous of Hermione's close friendship with Harry or her academic achievements. In the wizarding world, relationships can be complex, and Ginny might feel overshadowed by Hermione at times.
It could strain their friendship. Yelling is not a positive form of communication, and it might make Ginny feel attacked. She could become defensive and start avoiding Hermione. On the other hand, if Ginny understands Hermione's reasons, it could lead to a deeper conversation and actually strengthen their bond. For example, if Hermione yells because she's worried about Ginny's safety, Ginny might realize how much Hermione cares.
On the other hand, it could also be a turning point for the better. If they talk about what led to the yelling, they might clear up misunderstandings and become closer. For example, if Ginny was yelling out of fear for Hermione's safety in a dangerous situation, Hermione might realize Ginny cares deeply for her.
Hermione might run away crying. This would be a common reaction as she is a sensitive person. She could then go to Harry for support, and they might come up with a plan to resolve the issue with Molly.
In many fanfictions where Hermione confronts Ginny Weasley, it often stems from a conflict over a boy, like Harry. Hermione might feel that Ginny is being too forward or not taking Harry's feelings into account. For example, if Ginny is making big moves on Harry without considering how it affects his studies or his mental state, Hermione, being the practical and studious one, could confront her. It could also be about their different personalities clashing in the context of the wizarding world's social dynamics.
Maybe Hermione made a mistake that Molly thought was unforgivable in the context of the wizarding world. It could be something related to magic use that goes against the Weasley family's values. For instance, if Hermione experimented with dark magic in a way that Molly feared could endanger her family or the wizarding community.
I'm not sure specifically if there is a fanfiction with exactly that premise. But given the vast world of fanfiction, it's very possible. It could be an interesting take on the characters, but also a rather strange one considering Ginny and Hermione are friends in the original story. Maybe in this fanfiction, the author has a unique backstory or reason for Ginny to be 'out to get' Hermione, like a misunderstanding or some new plot device.
They are popular because they are both strong female characters. Ginny is brave and talented in Quidditch, while Hermione is extremely intelligent. Their different strengths make for interesting combinations in fanfiction stories.
Ron could be one of the main characters. Since he is Hermione's boyfriend and Ginny's brother, he might be caught in the middle of their conflict. He could try to play the peacemaker or end up taking sides, which would further complicate the situation.