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.
On Naruto's side, he would probably feel guilty after realizing what he had done. This guilt could make him try to make amends, but Sakura's initial reaction of anger and hurt would still be a big obstacle in their relationship. Their interactions would be filled with tension and awkwardness.
Maybe she's frustrated with Naruto. He might have done something really annoying like being overly loud or messing up a mission in a big way.
Well, one possible consequence could be that Naruto is seriously injured. Maybe he has a broken bone or gets knocked out cold. It could also lead to some sort of rift between them, with Naruto feeling betrayed by Sakura's overly aggressive action.
A reason could be that Sakura says something really hurtful to Naruto about his dreams or his abilities. Naruto, who has always been sensitive about those things deep down, might lose his temper and punch her.
In the fanfic, Sakura might be influenced by some dark force or a bad character. She starts to act against Naruto and their friends. Naruto, being the hero, tries to reason with her first but when she attacks him, he punches her back. This punch snaps her out of the influence, and they join forces again to fight the real enemy.
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 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.
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.