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.
The fanfiction might change the dynamic between Harry and McGonagall. For instance, if it creates a situation where McGonagall distrusts Harry without good reason, it would make sense for Harry not to like her in that fanfiction. Harry values the trust and respect he had with her in the original story.
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 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 could be that the fanfiction is set in a different universe where the characters' personalities are slightly altered. So, this 'new' Harry just doesn't click with Ginny in that version. For instance, if the fanfic is a darker take on the story, Harry might be more jaded and not open to a relationship with Ginny.
One reason could be a change in Dumbledore's personality. If he's depicted as being cold or distant in fanfiction, Harry, who knew him as a mentor figure, might not like it.
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.
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.
The fanfic might be set in an alternate universe where Ron has a different personality. If this new personality clashes with Harry's values or his own personality, then Harry may not like Ron. For example, if Ron is made to be more self - centered in this fanfic, Harry might find it hard to get along with him.
Perhaps she has her own vision of their relationship and doesn't want it to be influenced by the often - strange and varying ideas in fanfiction. Fanfiction can be full of outlandish concepts that she doesn't want to be part of. She wants to preserve the unique and special nature of her relationship with Edward as it is in real life.
It could be that in fanfiction, Snape has been through some additional trauma or experiences that change his perception of Lily. For instance, if he discovers something about Lily that he doesn't like, such as her involvement in some secret or her having a different side to her character that he finds unappealing. This would cause him to dislike her, as opposed to his more nuanced feelings in the original story.
One reason could be that the fanfiction changes Kakashi's teaching methods too much. Naruto is used to Kakashi's unique style in the original story, and if it's drastically altered in a way that doesn't seem right to Naruto, he might not like it.