It could be due to a misunderstanding. For example, Neji might have been wearing something different that day, or his hair was styled in a way that made Naruto think he looked more feminine. Or perhaps Naruto overheard some other characters making a comment about Neji that led him to make that joke. Another possibility is that Naruto is trying to break the ice in an awkward situation. If there was some tension between them or in the group, Naruto's off - hand comment could be his way of lightening the mood.
Maybe Naruto is just teasing Neji. In the Naruto world, friends often playfully taunt each other. Naruto might have seen Neji do something that he thought was more like what a girl would do, like being overly cautious or having a particular grace in his movements. It could also be a random joke that Naruto came up with to get a reaction out of Neji.
One possible reason could be Kakashi's strict teaching methods while not always following his own advice. For example, he might tell Naruto to always be on time for training but be late himself sometimes.
Neji might get angry. He's a proud character, and being called a girl in a somewhat derogatory way (if that's how he takes it) could make him lash out at Naruto. He could give Naruto a cold stare and tell him to watch his words.
Jealousy could be a reason. Suppose Neji has achieved something that Naruto desperately wants, like a high - ranking position in the village or a special recognition. Naruto's envy could turn into anger and fuel a fight where he overpowers Neji. Another reason could be a misunderstanding. Maybe Neji is wrongly accused of something that Naruto holds dear, like endangering a friend. Naruto, in his haste to protect and seek justice, attacks Neji with full force.
One possible reason could be that Naruto has some sort of new power that seems menacing or uncontrollable to Sakura at that moment. Maybe it's a power he got unexpectedly and it has some sort of dark or wild aspect to it that makes her blurt out 'demon'.
One possible motive could be a dark or alternate universe take. Maybe in this fanfic's world, there is some sort of dark magic or mind control that forces Naruto to do it against his will.
One possible plotline could be that Naruto has a sudden and extreme power-up that makes him overconfident. This overconfidence leads him to challenge Neji in a spar that gets out of hand and he ends up 'destroying' Neji in the sense of completely overpowering him. Maybe Naruto has unlocked a new form of his chakra that Neji can't counter with his Gentle Fist technique.
Well, perhaps Naruto, having grown up without his real mother, is seeking some kind of maternal connection. And the Kyuubi, being such a powerful and dominant force within him, fills that void. It could also be that Naruto senses a deeper, more primal bond with the Kyuubi, something that goes beyond just being a host and a tailed beast, and he associates that bond with a mother - child relationship.
One reason could be curiosity. Naruto might be curious to see how fans imagine different scenarios in the Naruto Shippuden universe. Maybe he wants to see how others view his friends and his own adventures.
One possible reason could be Naruto's out - of - control power. If in the fanfiction Naruto has some new and extremely powerful abilities that he can't fully manage, Sakura might see him as a monster out of fear. For example, if he accidentally causes destruction while trying to save the village.
Yes, there might be such fanfics. One possible reason could be exploring alternative storylines. Writers might want to break the traditional view of Naruto's loyalty to Konoha to create more complex and unique plot twists. For example, they could be imagining a scenario where Naruto discovers some dark secrets about Konoha that make him question his loyalty.