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.
Sakura might be under some sort of external pressure. For example, if there are certain expectations from her family or village that conflict with her relationship with Naruto. In order to conform to these expectations, she could end up saying or doing things that hurt Naruto's feelings. Another possibility is that she is jealous of Naruto's growing power or popularity and her insecurities lead her to hurt him.
Perhaps Sakura has been influenced by some false information or rumors about Naruto. If she hears something negative about him that she believes, it could cause her to act in a way that hurts his feelings. Also, she could be in a bad mood or having a rough time herself and unfortunately take it out on Naruto without really meaning to, but still causing him emotional pain.
Perhaps in the fanfiction, Naruto has had some bad experiences with Sakura. Maybe she has let him down in crucial situations, like not believing in him when he needed it most. This could lead to his feelings of despise as he feels betrayed by her lack of faith.
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.
It could be that Sakura has done something that has disappointed Naruto deeply. This could range from her making a decision in a mission that Naruto didn't agree with, to her not being there for him during a difficult time. These actions might have gradually eroded his love for her.
One possible reason could be miscommunication. Maybe Annabeth said something without realizing how it would come across to Percy. For example, if she was stressed about a quest and snapped at him when he was just trying to be helpful.
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 Naruto is focused on his own goals like becoming Hokage and he might see Sakura's feelings or her actions as distractions. He has a lot on his plate and may not have the time or energy to deal with her in a warm way.
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.
Another reason might be miscommunication. Harry has a lot on his plate, and sometimes he might not express himself clearly. He could say something that Ginny misinterprets as hurtful, when in fact he didn't mean it that way at all. For instance, he might make a comment about her Quidditch skills that she takes the wrong way.