It could be due to a discovery she makes that shocks her. Suppose she finds out that there's a traitor in their midst, or she uncovers a dark secret about Hogwarts that the others don't know. Her natural reaction would be to yell out in surprise and alarm.
Maybe she's yelling at Ron. Their relationship in fanfictions can be quite complex. If Ron says something insensitive or does something stupid, like forgetting an important task that could put their mission in jeopardy, Hermione would surely yell at him.
Maybe Albus has done something dangerous or disobeyed Harry's instructions. For example, if Albus got involved with some dark magic related stuff without Harry's knowledge, that would surely make Harry yell at him.
Maybe James Sirius Potter did something really reckless. For example, he might have put himself in danger while exploring some forbidden areas in Hogwarts. Harry, having gone through a lot of dangerous situations himself, would be worried and yell out of fear and frustration.
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.
One possible reason could be Snape's unfair treatment of Gryffindor students in the fanfiction. Hermione, being a strong advocate for justice and fairness, might not be able to tolerate his constant bias against her house. For example, if Snape gives Gryffindor students harsher punishments than students from other houses for the same infractions, Hermione would likely be furious and yell at him.
One possible reason could be that Mrs Black's old - fashioned pure - blood views conflict with Hermione's more inclusive and progressive ideas. Hermione, being a Muggle - born witch, might not tolerate Mrs Black's snobbish and discriminatory remarks about non - pure - blood wizards and witches.
Perhaps Snape was being overly harsh with one of Hermione's friends. She is very protective of Harry and Ron. If Snape said something mean or did something to harm them, Hermione would surely stand up and yell at him. For example, if he gave Ron a particularly difficult detention for no real fault of his own.
Perhaps in a 'harry potter yells fanfiction', Harry yells when he discovers that someone has been spreading false rumors about his friends. He could be in the Great Hall, stand up, and yell at the perpetrator, creating a big scene full of drama and conflict within Hogwarts.
It could also be a form of magical restraint. In some fanfictions, there are new and powerful dark spells that require the victim to be tied up physically as well as magically bound. Hermione, being a Muggle - born and a very powerful witch, might be targeted by those who want to use her magic for their own evil purposes. So they tie her up to subdue her and try to break her will to resist their magic - stealing attempts.
One possible reason could be that Harry did something reckless without consulting Hermione. For example, if he went off on his own to face a dark wizard, Hermione, being the cautious and logical one, would be furious. She values planning and teamwork, and Harry's solo actions might seem to her as endangering himself and others needlessly.
Maybe Adrien yells at Chloé because she's being mean to Marinette again. Chloé has a history of bullying Marinette, and Adrien, being Marinette's friend, might not tolerate it any longer and thus yells at Chloé in the fanfiction.