One possible scenario is that Minato was resurrected in a wrong way in the fanfiction. His behavior after resurrection was not what Naruto expected. Maybe he was more cold - hearted or seemed to have different priorities that didn't include Naruto, so Naruto started to hate him.
In some fanfictions, Minato could be shown as having abandoned Naruto not just physically (by dying) but also in a more emotional or spiritual sense. For example, if there were otherworldly forces at play and Minato made a choice that Naruto felt was a betrayal, like choosing to side with some entity that was against Naruto's interests. This would lead to Naruto hating him.
One scenario could be that Naruto discovers some hidden secrets about Minato and Kushina that he interprets as them being selfish. For instance, he might find out that they had a choice to be with him but chose something else instead, which makes him angry and full of hatred towards them.
One possible scenario is if Naruto is constantly blamed for the team's failures. For example, if every mission that goes wrong is pinned on Naruto, even when it's not his fault, he might start to hate the team. This could be due to a misperception by the other members or a malicious plot within the fanfiction world.
One possible scenario is when Naruto travels back in time in the fanfiction. He might end up looking like Minato as a result of some time - traveling magic or jutsu side - effect. This could lead to all kinds of interesting situations, like his friends not recognizing him at first.
It might be due to jealousy. If Minato was getting more attention or praise in the village for his achievements while Kushina felt overlooked, that could create resentment. Say, Minato was constantly being hailed as a hero for his speed and battle tactics, and Kushina, who also had great power, felt like she was in his shadow.
One possible reason could be that Naruto discovers some long - hidden secrets about Minato that he feels betrayed by. For example, if he found out Minato had made a deal that affected Naruto's life negatively in some way, like with the Kyuubi. Maybe Naruto feels that Minato sacrificed him for the greater good of the village without really considering his future or feelings.
Perhaps in the fanfic, there is a prophecy that says Naruto's friends will be the cause of his downfall. So, Naruto, fearing for his future and the safety of the village, starts to distance himself from them and eventually hates them. Or maybe his friends accidentally cause the death of someone Naruto loves dearly, which makes him unable to forgive them.
Perhaps in the fanfiction, Scott falls in love with someone that Stiles also has feelings for. This love triangle situation could turn Stiles' feelings into hatred as he sees Scott as a rival for the person he cares about. Also, if Scott accidentally reveals one of Stiles' secrets that he promised to keep, Stiles would likely be very angry and could start to hate Scott.
It could be that Percy gets involved in a conflict where he sides against Artemis' hunters. His actions in this conflict might make Artemis view him as an enemy. For example, if he accidentally harms one of her hunters while trying to protect someone else, she may grow to hate him.
Perhaps in the fanfiction, Sirius gets involved with the wrong crowd. And Harry, who has a strong sense of right and wrong, can't stand being associated with Sirius any longer. Or maybe Sirius has a falling out with one of Harry's other important people, like Hermione or Ron, and Harry takes their side and starts to hate Sirius as a result.
One possible reason in fanfiction for Naruto hating Minato could be the lack of a normal family life. Naruto was alone most of his life, not knowing his father. If he were to find out about Minato's actions in a negative light, like seeing the sealing as a selfish act to save the village at his expense, he could develop hatred. Fanfictions often take these complex emotions and build stories around them.