It could be related to a mission. If the mission required Kurenai to sacrifice someone for the greater good and Naruto was the most expendable in her eyes at that moment (although this is very unlikely given her character). Or maybe Naruto disobeyed a direct order from Kurenai during a mission which put the whole team in danger, and as a result, she had to take drastic measures to stop him which led to him getting hurt.
One possible reason could be a misunderstanding. Maybe Naruto was misidentified as a threat in a tense situation. For example, if there was some sort of dark jutsu at play that clouded Kurenai's judgment and made Naruto seem like an enemy. Another reason might be that Kurenai was under some sort of mind - control. There are many villains in the Naruto universe who are capable of such things. If she was being controlled, she might unknowingly attack Naruto.
Perhaps it was an accident during a training session. Kurenai could have been teaching Naruto a new jutsu or combat technique, and things got out of hand. Naruto might have made a wrong move, and in an attempt to correct him or protect herself, Kurenai accidentally hurt him. It could also be that there was some sort of emotional turmoil within Kurenai. Maybe she had received some bad news or was dealing with some unresolved issues, and Naruto just happened to be in the wrong place at the wrong time and became the target of her outburst.
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 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 storyline could be that in a mission gone wrong, Kurenai accidentally uses a jutsu that ends up hurting Naruto. Maybe she misjudges the situation and her genjutsu affects Naruto in an unexpected and harmful way.
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 Tsunade received some false information about Naruto that made her think he was a threat to the village, so she took actions that ended up hurting him.
Maybe she's been possessed. In some fanfictions, characters can be taken over by dark forces. So Kushina could be under the control of some evil entity and that's why she hurts Naruto.
One reason could be a powerful new enemy. Maybe an enemy with a unique jutsu that catches Naruto off - guard. The consequence would be that his friends would be extremely worried. They would probably rush to his side to protect him and find a way to heal him. His enemies might also take advantage of his weakened state to launch more attacks on the village.
He might be shocked at first. Naruto is used to seeing Kurenai as an ally, so being hurt by her would be unexpected. He could immediately ask her why she did it. If it was a serious injury, he might struggle to stay conscious while trying to understand the situation.
It could be related to their different personalities. Naruto is very outgoing and impulsive, while Kurenai is more calm and reserved. In the fanfiction, their clashing personalities might lead to Naruto developing a dislike for her. Naruto might feel that Kurenai is too strict or unapproachable, which causes him to hate her.
One possible reason could be a misunderstanding. Maybe Rias mistakes Naruto for an enemy due to some misinformation. For example, if there's a false rumor that Naruto is planning to attack her group. Another reason might be that Rias is forced to hurt Naruto under some sort of mind control or external pressure. It could also be a situation where Naruto accidentally gets in the way of Rias while she's dealing with a more powerful threat and she has no choice but to harm him in the process.