One reason could be a false accusation. If Spiderman is wrongly accused of a crime by the Avengers or someone within the Avengers' circle, he might feel betrayed and lash out at them. He's just a young hero, and such a false accusation could really make him angry.
Maybe in the fanfiction, Spiderman has joined a different group with different ideals. This new group might be against the Avengers for some reason, and Spiderman, being part of it, has to fight the Avengers. It's like he's caught in the middle of two conflicting sides and has to choose where he stands.
In some fanfictions, there could be an alternate reality or dimension where the normal relationships between Spiderman and the Avengers are reversed. Here, Spiderman might be from a place where the Avengers are seen as the bad guys, so he would naturally try to hurt them as part of his 'heroic' duties in that particular reality.
Well, in some fanfics, it could be a power struggle within the team. Spiderman might have new powers or knowledge that the other Avengers are jealous of or afraid of. So, they might take actions that end up hurting him, like trying to isolate him or directly attacking him in a fit of rage or fear.
Miscommunication. The Avengers could receive wrong information about Steve's actions or intentions, leading them to believe he's a danger and thus hurt him.
One possible reason could be that Tony initially misunderstands Spiderman's actions. He might think Spiderman is doing something wrong when in fact he's not, and then later realizes his mistake and tries to make it up by helping him. For example, if Spiderman is involved in a situation where it looks like he's causing destruction, but it's actually part of a bigger plan to stop a greater evil.
Well, perhaps Spiderman is poisoned by a new type of toxin from a villain. The Avengers then scramble to find an antidote. Black Widow uses her espionage skills to track down the origin of the toxin, while Hulk, in his Banner form, tries to analyze it scientifically. Thor might also use his Asgardian knowledge to see if there are any magical cures. In the meantime, they keep Spiderman comfortable and safe from further attacks.
One reason could be a misunderstanding. Maybe some villain has tricked Hulk into believing Spiderman is a threat. For example, the villain might have faked some evidence to make it seem like Spiderman was planning something bad against Hulk or his friends.
In some fanfiction, Spiderman might hurt the Avengers due to mind control. For example, if a powerful villain like Loki gets hold of Spiderman and forces him to fight against the Avengers, he could cause harm. Another possibility is a misunderstanding. Spiderman might be tricked into believing that the Avengers are a threat and act accordingly.
One reason could be to explore the darker side of the characters. Some fans like to see how the Avengers could be pushed to their limits and do something out of character, like hurting Tony as a teenager. Another reason might be to create a more angsty and emotional story, with Tony as a victim and the Avengers as the antagonists, which can add a lot of drama.
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 reason is that batjokes may not fit the mood of the fanfiction. Fanfiction often has its own atmosphere and theme. If batjokes are too comical or out of place in a more serious - themed fanfiction, it can ruin the overall feeling. For example, in a dark and gritty Batman - related fanfiction, a silly batjoke can break the immersion.
Perhaps there is a powerful artifact that both Spiderman and the Avengers are after. They end up in a conflict over it. Spiderman, with his street - smart ways, tries to outwit the Avengers and get the artifact for himself, believing he can use it for good in his own way.