Perhaps there was a dark secret about Naruto's origin that was revealed in a way that made others fear him. For example, if it was discovered that he had some connection to a feared enemy or an ancient evil. This could lead to his betrayal as people's fear overrode their previous loyalty to him. Also, jealousy among his peers could be a factor. If Naruto was constantly getting stronger and more popular, some might have become envious and were easily convinced to turn against him.
One possible reason could be a misunderstanding. Maybe Naruto is forced into a situation where he has to take actions that seem like a betrayal to the Uchiha. For example, if there are political forces at play that make Naruto choose between the safety of the village as a whole and the specific interests of the Uchiha clan. Naruto, being a firm believer in the village's unity, might make a choice that the Uchiha perceive as betrayal.
Well, in some fanfictions, it could be part of a much larger conspiracy within the Ministry of Magic. There could be a group within the ministry that has gone rogue and they see Harry as a symbol of resistance against their corrupt plans. So, they betray him to silence him and make an example out of him. They might also think that by getting rid of Harry, they can better control the wizarding population who often look up to Harry as a hero.
Perhaps there was some sort of dark influence or mind - control at play. An enemy might have manipulated Kakashi's mind in such a way that he believed Naruto was a threat and thus left him for dead, not realizing his true self.
One possible reason could be a misunderstanding. Maybe they were misled by false information or an enemy's trickery that made them think Naruto was a threat at that moment. Another reason might be extreme pressure or a life - or - death situation where they thought sacrificing Naruto was the only way to save the rest of the team or complete a crucial mission.
One possible reason could be that Kushina was forced to leave Naruto due to some external threat she thought would endanger him more if she stayed. For example, if there were powerful enemies after her and she feared they would use Naruto to get to her.
Well, in some fanfictions, it could be due to political manipulation. After the war, there might be different factions vying for power. Naruto could be seen as a threat to certain groups, and they manipulate his friends into betraying him. Also, sometimes characters' insecurities can play a role. His friends might have their own personal issues and insecurities that lead them to turn on Naruto.
Maybe Naruto is left behind in training because the instructor misjudges his abilities. As a result, Naruto starts training with a retired ninja who teaches him some old - fashioned but effective techniques. This gives him an edge when he finally rejoins his group.
Well, it might be about Naruto growing up without Kushina's presence. Maybe he has to face challenges alone and discovers things about his mother in the process.
Maybe Naruto is betrayed by someone within the village who sets him up to look like he's dead. Left for dead, he's found by a hermit who teaches him new and powerful jutsu. With his new skills, he plans to return to the village to expose the traitor and prove his worth once again.
One possible reason could be fear. Naruto is extremely powerful, and some in Konoha might fear that he could one day lose control of his power. Another reason could be political intrigue. There may be certain factions within Konoha that see Naruto as a threat to their power and influence. Also, jealousy might play a part. Naruto has achieved so much and has the love of many, and some might be jealous and thus plot against him.