It could also be due to some actions of McGonagall that seemed suspicious to Harry. Perhaps she made a decision regarding Hogwarts or Harry's safety that Harry didn't fully understand at the time. In the complex world of the wizarding school, decisions are often made with many factors in mind, but Harry might not be aware of all of them, leading to his distrust.
Another factor could be external influence. If there are dark forces at work, they might try to plant seeds of doubt in Harry's mind about McGonagall. They could spread false rumors or create situations that make it seem like McGonagall can't be trusted. This would play on Harry's natural paranoia, especially given his role in the fight against the dark side.
It could also be that in the fanfiction, McGonagall has shown some form of bias. Maybe she seems to favor certain students or groups over others, and Harry, being the one who always stands up for fairness, starts to distrust her when he notices this behavior. He might feel that she is not as just as he once thought her to be.
It could also be due to a series of unlucky events. Suppose Hermione's well - intentioned plans keep backfiring in a way that makes Harry question her judgment. Like when she tries to solve a problem but ends up making it worse, Harry might start to lose trust.
McGonagall might notice Harry's distrust and feel hurt or frustrated. She may try to figure out what went wrong but find it difficult as Harry is not forthcoming. Their interactions become less warm and more formal. For example, in class, Harry may be less likely to ask for help from McGonagall, and McGonagall may be more strict with Harry as she doesn't understand his change in attitude.
Perhaps there were some secrets that Ron was keeping from Harry. In the wizarding world, secrets can be a big deal. If Ron had a secret related to his family or some other important matter and Harry found out about it in a way that made it seem like Ron was hiding something bad, it could lead to Harry not trusting him. Also, Ron's friendship with other characters might make Harry jealous or suspicious. If Ron was getting closer to someone Harry didn't trust, it could spill over and make Harry question Ron's loyalty to him.
One possible reason could be that Harry discovers some hidden actions of Dumbledore that seem manipulative. For example, if Dumbledore has been keeping secrets about Harry's past or his destiny without fully explaining them. Harry might feel used or deceived, leading to his distrust.
One possible reason could be that she is under some sort of dark magic influence. Maybe a spell has been cast on her that makes her act out of character and abandon Harry.
One reason could be the alteration of McGonagall's personality. If in fanfiction she is made to be overly strict or mean, Harry, who knows her real character, would dislike this new version. In the original series, McGonagall was strict but fair, and any deviation from that in fanfiction might be off - putting to Harry.
Maybe in that fanfiction, McGonagall has some actions that Harry misinterprets. For example, she might be too strict with him in a way that he can't understand at that moment.
One reason might be that the fanfiction doesn't capture the essence of Mcgonagall as Harry knows her. He has a deep understanding of her from their time at Hogwarts, and if the fanfiction misses that, he won't like it.
Maybe in those fanfictions, the author portrays McGonagall in a way that Harry doesn't like. For example, the character might be out of character and act too harshly or differently from how he expects her to be in the original story.