In some fanfictions, the author might create a situation where Harry's actions lead to great harm to Gryffindor as a whole. For instance, if he makes a decision that causes Gryffindor to lose a significant amount of points in a crucial time, like right before a major competition. This could lead to his censure as the house would see him as a liability. Also, if he gets into a feud with important Gryffindor figures, like the prefects or the head of the house, it could result in his censure.
In some fanfictions, it could be due to a misunderstanding. Maybe someone framed Harry for a serious rule violation that Gryffindor's house values highly, like cheating in an important magical exam. And the evidence against him seems so strong that the Gryffindor house decides to banish him.
In some fanfictions, it could be a political move within Hogwarts. There might be a group that wants to undermine Dumbledore's influence, and since Harry is so closely associated with him, they target Harry by getting him banished from Gryffindor. This could also be related to the discovery of some long - hidden secret about Harry's family that makes the Gryffindors view him differently.
Another reason could be related to a new prophecy. Suppose a new prophecy emerged that said Harry Potter's presence in Gryffindor would bring great danger to the house. The Gryffindor students and faculty, believing in the importance of protecting the whole house, might have decided to banish him. But of course, this would be a very difficult decision as Harry has been an important part of Gryffindor before. And in the end, the prophecy might turn out to be misinterpreted.
One possible reason could be a false accusation of using dark magic. In some fanfictions, the wizarding world can be very paranoid about dark magic, and if Harry was wrongly suspected of delving into it, Gryffindor might exile him to protect their reputation.
Maybe he's falsely accused of stealing important Gryffindor artifacts. For instance, if the Sword of Gryffindor goes missing and Harry is wrongly blamed, the house might decide to kick him out. It could be part of a plot by a jealous student or an outside force trying to disrupt Hogwarts.
One possible reason could be a fallout with his friends in Gryffindor. Maybe he feels betrayed by them in some way in the fanfiction world. For example, if they wrongly suspect him of something.
Perhaps he leaves Gryffindor in fanfiction because he is influenced by a new mentor or friend who is from a different house or group. This person might convince him that he can achieve more or be more true to himself outside of Gryffindor. Also, it could be due to a prophecy or a special mission that requires him to distance himself from Gryffindor for a while to protect the house or the entire Hogwarts from a certain threat.
One possible reason could be a serious rule violation. For example, if Harry was wrongly accused of using dark magic within the Gryffindor common room. Another reason might be that he was framed for stealing the Gryffindor sword. It could also be due to a conflict with other Gryffindor students that got out of hand and the house decided they couldn't keep him anymore.
One reason could be a falling - out with his friends in Gryffindor. Maybe there was a misunderstanding that grew so large that he felt he couldn't stay. Another possibility is that he might be lured away by some mysterious force or character who convinces him that Gryffindor is no longer the right place for him. For example, if a new group claims to have a better way to fight Voldemort and they are from a different 'house' in this fanfiction concept.
Maybe he was too busy dealing with the real threats in his life, like Voldemort and his Death Eaters. Fanfiction might seem unimportant compared to the real battles he had to face.