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 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.
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.
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.
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 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.
Well, it could strengthen their bond. Naruto being hurt might make Hinata more protective and caring towards him. This could lead to Naruto realizing Hinata's true feelings for him more deeply, and in turn, he might start to see her in a new light, growing closer to her.
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.
I like 'The Comfort After the Storm'. This fanfic focuses on Sakura dealing with Naruto's emotional pain after he loses a very important person. Sakura is there for him, and they have some really heart - to - heart conversations. It shows how their relationship can be so much more than just teammates.
In some Sasunaru fanfictions, Sakura might hurt Naruto emotionally. For example, if she chooses Sasuke over Naruto in a very cruel way, it can break Naruto's heart. She could say mean things about his dreams or his past as an orphan, which would deeply wound him.