It could be due to Sakura's feelings for Sasuke. If she's overly focused on Sasuke and Naruto gets in the way of her plans regarding Sasuke in some way, she might lash out and hurt Naruto without really meaning to cause serious harm.
One common reason is miscommunication. If Sakura misunderstands Naruto's intentions, she might react harshly and physically harm him. For instance, if Naruto tries to keep a secret from her to protect her, but she misinterprets it as betrayal.
One possible plotline could be that Sakura, perhaps under the influence of some dark force or a misunderstanding, physically attacks Naruto. This could be due to a false belief that Naruto has done something terrible to their village or friends. Another plotline might involve Sakura's words hurting Naruto deeply. For example, if she tells him that he will never be good enough or that she doesn't really consider him a true friend after all. It could also be that Sakura's actions in pursuit of Sasuke end up causing Naruto pain indirectly, like if she constantly ignores Naruto's feelings for her while she chases Sasuke, making Naruto feel unimportant and hurt.
One possible reason could be a misunderstanding. Maybe Sakura misinterprets Naruto's actions or words, thinking he has betrayed her or their friends in some way, which leads to her hurting him one last time in a fit of anger.
Perhaps in the fanfiction, there is a plot twist where Sakura has been brainwashed by an antagonist. The antagonist could be using her to get to Naruto, knowing their close relationship. So, she would then be made to attack Naruto without her own will. Or, there could be a prophecy or some sort of pre - determined fate in the fanfiction's plot that causes Sakura to hurt Naruto, even if she doesn't really want to.
One reason could be that Sakura is confused about her own feelings. Maybe she has feelings for someone else and doesn't know how to handle Naruto's obvious affection towards her, so she lashes out and ends up hurting him.
Well, in some fanfics, Sakura might be jealous of Naruto's growing power and relationship with others. So she could try to undermine him, which in turn hurts Naruto. Maybe she spreads false rumors about him in the village. Another idea is that Sakura is forced to choose between Naruto and Sasuke in a dangerous situation, and her choice, even if it's not completely her fault, ends up hurting Naruto deeply. It could also be that Sakura's overzealous medical treatment, in an attempt to save Naruto from a serious injury, actually causes him more pain and harm.
One reason is that some fanfiction authors may lack a deep understanding of Naruto's character. They might write things that are completely contrary to his values and personality just for the sake of creating a 'unique' story. For example, Naruto is known for his positive attitude and strong will, but in some fanfictions, he could be depicted as a negative or spineless character.
One possible scenario could be in a fanfic where Sakura accidentally uses her strength during a training session with Naruto and physically hurts him. Maybe she misjudges her punch or kick.
One reason could be jealousy. If Naruto is getting more attention or has achieved more in the ninja world, his sister might be jealous and this could lead to her actions that hurt Naruto, either by spreading false rumors or directly confronting him in a hurtful way.
One common theme is misunderstanding. Often, Naruto may misunderstand Sakura's intentions or vice versa, which leads to one of them getting hurt. For example, Naruto might misinterpret Sakura's concern for him as pity, and his reaction could hurt her.