It could also be due to a prophecy. The guild might have feared that Natsu's power was going to lead to something disastrous in the future. In some fanfictions, prophecies play a big role in guild decisions. So, they decided to banish him to try and prevent the predicted catastrophe.
One possible reason could be that he was wrongly accused of a serious crime within the guild. Maybe some powerful and influential members believed he was a threat and pushed for his banishment. For example, if there was a string of mysterious attacks and Natsu was framed as the culprit due to his often wild and uncontrollable nature in battle.
Often, it could be because of a false accusation. Maybe someone framed Natsu for a crime he didn't commit, like stealing a powerful magical artifact from the guild. So, to maintain peace and order, the guild leaders had no choice but to banish him.
One possible reason could be that he accidentally causes too much destruction during a mission. Maybe he loses control of his magic and wrecks an important place in the magical world, leading the guild to expel him as a form of punishment.
One possible reason could be that he's framed for a crime he didn't commit. Maybe someone planted false evidence to make it seem like he was endangering the guild. Another reason might be that his power got out of control and the guild, fearing for the safety of its members, made the tough decision to kick him out.
Another reason might be related to Naruto's loyalty being questioned. In fanfiction, there could be a plot where an enemy tricks the guild into believing Naruto has betrayed them. The Fairy Tail guild values loyalty highly, and if they think Naruto has sided with an enemy, they might banish him. For example, if an enemy uses some sort of illusion magic to make it seem like Naruto has attacked a guild member, this could lead to his banishment.
In a fanfiction, there could be a situation where Lucy is forced to side with a group that Natsu is against. This would make Natsu see her as an enemy. Or perhaps there is a prophecy that Lucy is involved in that Natsu misinterprets as something bad. He might think she is a threat to the guild or his friends. Also, if there is a love triangle situation where Lucy chooses someone else over Natsu in a way that really hurts his feelings, that could be a reason for him to start hating her.
Perhaps they leave because of a disagreement within the guild. Maybe there's a new policy or a decision made by the guild master that they don't agree with. For example, if the guild decides to get involved in a war that they think is unjust, they might choose to leave rather than participate against their beliefs.
One possible reason could be a misunderstanding within the guild. Maybe some false information was spread about them, leading others in Fairy Tail to turn against them. Another reason might be a power struggle. If Natsu and Erza were becoming too powerful, some jealous members could have conspired to make it seem like they were betraying the guild. Or perhaps an outside force manipulated the situation to drive a wedge between them and the rest of Fairy Tail.
One reason could be that some writers might want to create a more complex or darker storyline. By having Natsu be hated, it adds conflict. Maybe they portray him as having made a big mistake that the other characters in the fanfic can't forgive.
One possible reason could be a conflict with other guild members. Maybe there's a misunderstanding or a fight that makes Natsu feel he no longer belongs. Another reason might be that he has a personal mission that goes against the guild's rules or values in the fanfiction. He could also be framed for something he didn't do and, feeling betrayed, decides to drop out.
One possible reason could be a misunderstanding within the guild. Maybe someone spreads false rumors about Natsu, leading others to believe he's done something wrong. Another reason might be a power struggle. If there are those in Fairy Tail who envy Natsu's strength and popularity, they could plot against him to get him out of the way.