Sasuke could be one. Given their complex relationship, there could be a situation where Sasuke's newfound power or different ideology leads him to fight and beat Naruto in a fan - made story.
In some fanfictions, Naruto might get beat up when facing a powerful new villain who has some unknown jutsu. This could be a villain created by the fanfic writer to test Naruto's limits.
Orochimaru could also be a character to beat up Naruto in a fanfic. He's always been interested in the power of the Nine - Tails and Naruto as a whole. He might see an opportunity to capture Naruto and in the process, end up beating him up to subdue him.
Naruto might be shocked at first. He has always seen Sakura as a friend, so being beaten up by her would be unexpected. He could try to talk to her and figure out what's wrong.
One 'naruto beat up' fanfiction could be about Naruto facing a powerful new enemy in a hidden village and having to fight his way out. Maybe he uses new jutsu combinations to beat up the bad guys.
Often, it's other powerful ninjas from rival villages. For example, shinobi from the Hidden Mist Village might be opponents. They could have unique abilities that Naruto has to overcome to beat them up.
Well, in a lot of these fanfictions, Stiles can get beat up due to his own recklessness. He might be so determined to solve a mystery or help his friends that he doesn't think about the consequences and ends up in a dangerous situation where he is outnumbered and beaten up. Also, there could be miscommunication. Maybe someone thinks he has done something wrong when he actually hasn't, and they take matters into their own hands and beat him up.
One possibility is that there's a misunderstanding between Naruto and Karui. Maybe Karui thinks Naruto has something to do with Sasuke's actions that have affected her village. So, in her anger, she attacks Naruto.
Maybe some new kids in the neighborhood who are trying to establish their dominance and pick on Lincoln as an easy target. They might not know much about him or his family, but just see him as someone they can bully.