Another reason could be related to a hidden curse or spell. In a certain fanfiction, an old family curse is placed on Hermione without her knowledge. As it starts to take effect, one of the symptoms is fainting. This then leads to a whole mystery for Harry and Ron to solve as they try to figure out what's wrong with her and how to break the curse.
Well, it might be part of a fantasy world created by the author where unusual circumstances bring Harry and petrified Hermione together. Maybe it's to create tension or drive the story in an unexpected direction.
One reason could be his status as the main character in the original series. He is the 'Chosen One', so fanfiction writers may be more inclined to center their stories around him.
Maybe Molly was really angry at Hermione for something she did. That could be the reason for sending the Howlers.
Maybe Harry accidentally cast a spell on Hermione during a training session that caused her some harm. So he feels guilty because he didn't mean to hurt his friend.
Perhaps he has feelings for Hermione that he doesn't know how to handle. Harry might be afraid of these new emotions and so he acts cold as a defense mechanism. In some fanfictions, there could be a plot device where Harry has seen a vision of the future that makes him think being close to Hermione is dangerous for her. So, in an attempt to protect her, he acts cold. It could also be that there is some external pressure, like from other students or even teachers, that makes Harry think he should distance himself from Hermione, and this shows as cold behavior.
It could be a plot device to create drama. For example, if there's a love triangle situation and Harry faints on Ginny, it can stir up all sorts of emotions among the characters involved. It might also be because of some sort of dark magic that has been affecting Harry secretly and Ginny is the trigger point for him to finally succumb to it. This can then lead to a whole mystery - solving plotline in the fanfiction.
Some writers might create such fanfiction for the shock value. They want to break the established strong friendship in the original series to get readers' attention.
Maybe because in those fanfictions, Hermione's bossy character is over - emphasized. Harry might feel like it doesn't stay true to their real friendship dynamic in the original series.
In some Naruto fanfictions, Naruto might faint due to overusing his chakra. For example, if he pushes himself too hard in a battle, like when he tries to use a new and extremely powerful jutsu without fully mastering it. His body can't handle the excessive chakra drain, and he faints as a result.
A really interesting 'Harry Potter Hermione and Harry fanfiction' is 'A Different Path'. In this story, the author takes a different turn on the events after the Battle of Hogwarts. Harry and Hermione's relationship becomes more of a partnership in rebuilding the wizarding world. 'The Lost Prophecy' is also good. It focuses on a new prophecy that involves only Harry and Hermione, leading them on a dangerous and exciting adventure. And 'Shared Secrets' where they discover a long - hidden secret that changes their understanding of their friendship and themselves.