One possible reason could be the intense pressure he feels to protect the village. He might overexert himself in training and accidentally hurt himself. Another reason could be self - punishment for not being able to save someone. In some fanfictions, Naruto might feel guilty about a comrade's death and take it out on himself through extreme training or dangerous missions.
In some fanfictions, Naruto could be under a genjutsu that makes him harm himself. For example, an enemy might have cast a powerful genjutsu on him that distorts his perception of reality, making him think that he needs to do harm to himself in order to achieve a certain goal. Also, if he discovers some dark secrets about his family or the village, it could lead to an emotional breakdown and self - harm.
Perhaps Sakura is in a state of extreme stress. Maybe she has a lot of pressure on her, like trying to save a village or a loved one, and Naruto's actions, which might seem reckless to her at the time, cause her to snap and hurt him without really meaning to.
Snape could be distracted by his own dark thoughts or memories. For example, if something reminded him of his past with James Potter, his hatred for Harry's father might cloud his judgment for a moment and cause him to accidentally cast a spell in Harry's direction.
Perhaps Natsu is under the influence of a powerful and dark magic that makes him lose control of himself and accidentally hurt Lucy. It could also be that Natsu is trying to protect Lucy from something but his actions end up causing her harm instead. Like if he tries to keep her away from a dangerous situation by pushing her too hard and she gets injured.
One possible reason could be stress. In fanfic scenarios, she might be under a lot of pressure from her scientific research or protecting the Earth. The stress could build up to a point where she starts to harm herself as an outlet.
It could be that she sees the pain she caused Harry and it makes her feel guilty. In the story, perhaps she was influenced by others' opinions of Harry and didn't trust her own long - standing friendship with him. When she finally comes to her senses, she regrets all the hurtful things she said or did.
In some fanfictions, it might be part of a plot to create tension. The writer wants to show that their relationship isn't all smooth sailing. So, Katara hurting Aang can be a device to make the story more interesting. It could also be related to different character arcs, like Katara trying to become more independent and in the process, her actions accidentally harm Aang.
Perhaps in the fanfiction, Kakashi is influenced by a dark power. This power corrupts his mind and makes him turn on Naruto. It could be related to some ancient curse or a new enemy's ability that targets Kakashi's mental state. Naruto, being the target, would then be at the mercy of Kakashi's attacks, creating a lot of drama and conflict in the story.
Well, it could be a situation where Hinata is trying to protect someone else from Naruto, perhaps believing he is a threat at that moment due to some false information. She might then end up hurting him while trying to fend him off. Or, in a darker fanfiction, there could be an alternate universe where Hinata has turned evil and deliberately targets Naruto to cause him harm.
Another possibility is that Naruto was trying to protect someone else from Sasuke. Suppose Sasuke was on a path that would endanger another important character in the story, like Sakura. Naruto, in his eagerness to safeguard Sakura, might have accidentally hurt Sasuke while trying to stop him from taking any harmful actions.
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.