It could be a new villain that has emerged. This villain might have some sort of vendetta against Steven specifically, perhaps because of his unique powers or his role in the gem world.
A fanfiction could be written where Steven gets hurt in a more emotional way. For example, he discovers some dark secrets about the Gems' past that are so shocking it causes him mental and emotional pain, which in turn affects his physical well - being. His friends notice the change in him and try to help him come to terms with what he has learned.
There are also the possibility of some inter - dimensional beings. In the Ben 10 universe, there are many different dimensions. If a being from another dimension comes through with the intention of causing chaos, they could target Ben. They might have powers that are completely foreign to Ben and his allies, making it difficult for him to defend against them. And let's not forget about the possibility of some of Ben's old enemies teaming up. If they work together, they could come up with a plan to really hurt Ben, whether it's physically or by ruining his reputation among the people he protects.
There could be a new character in the fanfiction, like a bully who targets Lincoln just because he seems like an easy target and ends up hurting him.
Perhaps it's a mysterious figure in the fanfiction world. This unknown character could have some ulterior motives against Jacob and find ways to hurt him, like setting traps for him.
Steven could get hurt while experimenting with his powers. He might push himself too far in an attempt to discover new abilities or to use his existing ones in a more powerful way. This overexertion could lead to him getting physically or mentally hurt. Also, he could be hurt by a Gem who has a vendetta against the Crystal Gems and targets Steven as a way to get back at them.
A mysterious new enemy that has infiltrated the village could be the cause. This enemy might be on a mission to disrupt the balance in the ninja world and sees Sarada as an obstacle. They could attack her when she is alone or on a solo mission. Their motives could be related to some ancient grudge against her family or the village as a whole.
One scenario could be that Steven is exploring an unknown area and stumbles upon some sort of dangerous trap that causes him harm. It could be a hidden energy field or a collapsing structure. Another possibility is that he gets hurt while trying to protect his friends. He might jump in front of an attack meant for someone else, like Connie or the Crystal Gems, and bear the brunt of the injury.
Even some of the school faculty could be responsible in a sense. For instance, a strict teacher who doesn't understand Danny's situation might push him too hard during detention or some other punishment, which could lead to an accidental injury. Or a science teacher's experiment could go wrong and Danny could get caught in the crossfire.
Sometimes, it could be due to her own actions. Lydia might be overconfident and take risks that she shouldn't. For instance, she could try to perform a very difficult and dangerous magic spell without proper training, and it backfires, causing her to get hurt.
It could be a villain in the fanfiction. Maybe a new, powerful vampire who has a vendetta against Bella or her friends.