One possible reason could be Naruto's out - of - control power. If in the fanfiction Naruto has some new and extremely powerful abilities that he can't fully manage, Sakura might see him as a monster out of fear. For example, if he accidentally causes destruction while trying to save the village.
Well, it could be that in this fanfiction, Naruto has some sort of hidden agenda. He might call Sakura ugly as a form of reverse psychology. He could be thinking that by doing so, she'll prove him wrong and become more confident. Or perhaps there's some miscommunication or misunderstanding between them. For example, Naruto misheard someone talking about Sakura in a negative way regarding her looks and he wrongly believes it, so he says she's ugly.
He could also get angry. After all, being misjudged like that is unfair. His anger could lead him to either lash out verbally at Sakura or he could leave the village in a fit of rage, feeling that he is not accepted even by his friends. This could then lead to a series of events where Naruto has to find his own way and Sakura realizes her mistake later on.
Maybe he's frustrated with her lack of progress in combat compared to him and Sasuke. He could also be in a bad mood and say it without really meaning it.
Perhaps there was some sort of dark influence at play. In the world of Naruto, there are often dark forces and genjutsu (illusion techniques). It's possible that Naruto was under the influence of a genjutsu that made him see Sakura as a threat, so he punched her in self - defense without realizing it was an illusion.
One possible reason could be that Sakura realizes she has different goals or values that are not compatible with being around Naruto. Maybe she discovers a new path in life that doesn't involve him, such as focusing on her own medical ninja career without Naruto's chaotic lifestyle interfering.
One possible reason could be that Naruto notices Sakura has been struggling with her medical ninjutsu skills lately and he believes an evaluation will help her improve. For example, she might have made some mistakes during a recent mission where her medical skills were crucial.
Well, in the fanfiction context, Naruto may not love Sakura because he has unrequited feelings for someone else. Maybe he has a deep connection with another character that makes him view Sakura just as a teammate. Also, their personalities might not be as compatible in a romantic sense as one would initially think. Naruto is often impulsive and headstrong, while Sakura can be a bit more reserved in some ways, and this could lead to a lack of romantic attraction.
One possible reason could be extreme jealousy. Sakura might be so blindly in love with Sasuke that she sees Naruto as a threat to Sasuke's attention or her relationship with Sasuke. Maybe she thinks Naruto is getting in the way of Sasuke's return to the village or her attempts to win Sasuke back.
One possible reason could be that she might have underestimated Naruto in the past. She often belittled his abilities and dreams, but as she grew and realized his true strength and determination, she felt the need to apologize for her previous behavior.
One possible reason could be a misunderstanding. Maybe Sakura said something that Naruto misinterpreted as being hurtful or dismissive of his feelings. For example, if she made a comment about his abilities in a negative way during a crucial moment, it could lead to him distancing himself.