A rogue ninja from a hidden village. Maybe a ninja who has a grudge against Konoha and sees Naruto as a symbol of Konoha's strength, so he targets Naruto and manages to beat him in the fanfiction.
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.
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.
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.
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.
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.
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.
It could be an antagonist character in the Septiplier fanfiction world. Maybe someone who has a grudge against Jack for some reason, like a rival in a game or a love interest situation gone sour.
It could be a new character introduced specifically for this fanfiction. Maybe a bully who has just transferred to Percy's school and takes an instant dislike to him. This bully might be jealous of Percy's popularity or has a grudge against him for no real reason other than wanting to assert dominance.
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.
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, perhaps Johnny made some mistake that angered Jally's group. Maybe he accidentally insulted Jally or got in the way of something Jally cared about. So Jally, with his friends, decided to teach Johnny a lesson by beating him up.