Another reason could be stress - related. Naruto has a lot of responsibilities, like being the Hokage. The stress of leading the village, dealing with political matters, and protecting everyone could manifest physically as back pain. His body might be reacting to the mental pressure he's under.
Maybe he got injured during a fight. In the Naruto universe, battles are fierce. If he was hit in the back by an enemy's jutsu or weapon, it could cause lingering pain. Say he was caught off - guard by an opponent's sneak attack from behind, that could easily damage his back.
It could also be due to a power struggle. Fem Sasuke might be jealous of Naruto's growing power and influence. In some fanfictions, characters can be driven by envy, and she might see Naruto as a rival that needs to be put in her place, so she ends up hurting him.
One possible reason could be a misunderstanding. Maybe Tsunade received some false information about Naruto that made her think he was a threat to the village, so she took actions that ended up hurting him.
Maybe she's been possessed. In some fanfictions, characters can be taken over by dark forces. So Kushina could be under the control of some evil entity and that's why she hurts Naruto.
It could be due to a misunderstanding. Perhaps there is false information circulating about Naruto that Tsunade believes. Like if someone spreads rumors that Naruto is involved in some dark plot, Tsunade, in her role as Hokage, might take hasty actions against him. Later, when she realizes it's all a lie, she regrets it.
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 that he ate something bad in the story. Maybe some spoiled food from a dodgy tavern in the fictional world.
One possible reason could be a misunderstanding. Maybe Tsunade misinterprets Jiraiya's actions or words. For example, if Jiraiya writes something in his book that Tsunade takes the wrong way, she might lash out at him. Another reason could be related to their past. If there are unresolved issues from their earlier days together, like an old argument or a failed mission where they had differences in opinion, it could lead to Tsunade hurting Jiraiya in the fanfiction. It could also be a situation where Tsunade is trying to protect Jiraiya in a strange way. She might think that by pushing him away or causing him physical or emotional pain, she is actually saving him from a greater danger that she foresees.
One possible reason could be an injury. Maybe he got into a fight or an accident in the fanfiction world that damaged his ribs or internal organs related to breathing. Another reason might be a disease or illness, like a severe respiratory infection.
One possible reason could be a misunderstanding. Maybe Superman is under the influence of some mind - controlling villain or a magic spell that makes him see Superboy as a threat when he really isn't. Another reason could be a difference in their ideologies. Superboy might have a more modern or radical approach to saving the world that Superman doesn't agree with, leading to a conflict that gets out of hand.
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.