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 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 she's under the influence of a powerful genjutsu. Genjutsu can distort one's perception and make them do things they wouldn't normally do. In this case, Kushina might be seeing Naruto as an enemy in the genjutsu and thus hurt him. Or it could be a test in a very extreme way. She might think that by putting Naruto through pain, she can make him stronger, although this is a very cruel way of thinking.
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 she was misled by false information about Naruto being a threat to the village. Another reason might be that she was under some kind of mind control. In some fanfictions, dark magic or evil entities can take over a character's mind and make them act out of character.
Another reason could be related to a prophecy. If there was a prophecy in the fanfiction that Naruto would bring great destruction in the future, and Kushina, being a self - sacrificing mother, might think that killing him is the only way to prevent that destruction, even though it goes against her natural love for her son.
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 possible reason could be jealousy. Maybe Molly is jealous of Hermione's intelligence and the special bond she has with Harry and Ron. Another reason might be that she feels Hermione is a bad influence on her sons in some way. For example, she might think Hermione's Muggle - born status could bring trouble to the family in the wizarding world which is full of pure - blood supremacist ideas.
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 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 reason could be the stress from her ninja life. Constant battles, the pressure to protect the village, and the fear of losing her loved ones can take a toll on her mental health. Another reason might be her relationship issues, especially her unrequited love for Sasuke which has been a long - standing source of emotional turmoil for her.