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.
In some fanfictions, Kakashi could be written to be too cold towards Naruto. In the original series, there is a bond between them, but if the fanfiction breaks that bond by making Kakashi unfeeling towards Naruto, Naruto would not like that portrayal of Kakashi.
It might be that the fanfiction gives Kakashi a different set of values that conflict with Naruto's. Naruto values things like loyalty, hard work, and friendship, and if Kakashi in the fanfiction goes against these values, Naruto would not like him. For example, if Kakashi is shown to be disloyal to the village in the fanfic, Naruto would surely dislike that version of him.
In certain fanfictions, Naruto might have a pre - existing relationship or unrequited love for someone else. This could make him overlook Hinata or even seem to dislike her because his heart is set on another character.
One reason could be that Naruto has always been more attracted to those who understand his outcast past better. Sakura doesn't really have that kind of connection with him as she comes from a more normal background. So there's a lack of that fundamental understanding between them which hinders any romantic feelings.
One possible reason could be that Kakashi is preoccupied with other important matters in the village. Maybe he has some top - secret missions or tasks assigned by the Hokage that demand his full attention, leaving him with little time to focus on Naruto.
One reason could be that he sees Naruto as a younger version of himself in some ways. Both have had their share of loneliness and challenges growing up. Kakashi may want to prevent Naruto from going through the same pain he did. Another reason is Naruto's importance to the village. As the jinchuriki of the Nine - Tails, Naruto is a key asset. Kakashi, being a loyal ninja, wants to protect the village's future which is tied to Naruto.
One possible reason could be that Naruto might feel Kakashi is too strict with his training. Maybe Kakashi's methods are too harsh for Naruto, making him frustrated and gradually developing dislike.
One possible reason could be Kakashi's reputation as a strict and powerful teacher. Naruto might be in awe of his skills and fear making mistakes in front of him.
One possible reason could be that Naruto might be trying to prove his independence. He has grown and wants to show that he can handle things on his own without always relying on Kakashi's guidance.
One possible reason could be that Naruto's character development leads him to focus more on other aspects like his ninja duties or his bond with other friends. As he grows, his priorities shift.
Well, Naruto has always been there for Sasuke in the original story. In fanfiction, Fem Sasuke might secretly like Naruto because she sees his loyalty. He's constantly trying to bring Sasuke back to the right path. This loyalty could translate into a deeper affection in the fan - created stories.
Perhaps the fanfiction alters the relationship between Kakashi and Naruto in a way that Kakashi doesn't like. Maybe it shows Kakashi as being overly harsh or unfair to Naruto in a situation where in the original series he wouldn't be. It could also be that the fanfiction contains plot elements that Kakashi, as a character, would find illogical or against the spirit of the Naruto world.