Perhaps some villain is constantly taunting him about his past, like being an orphan or not being strong enough in the beginning. This kind of provocation would make Naruto pissed.
It could be due to the failure of protecting his village or his loved ones. Naruto has always been about protecting those important to him. If he fails at that, his anger is understandable.
In some fanfictions, it might be because of jealousy. For example, if Rukia spends a lot of time with another character, Ichigo could get pissed. He might have feelings for her that he hasn't fully realized or admitted, and seeing her with someone else stirs up his anger.
Another reason might be related to his family. In some fanfictions, his parents' story or his relationship with his family members could be distorted. Harry has a strong connection to his family, especially his parents, and any wrong portrayal of that could make him pissed off.
Sasuke could be the cause. If Sasuke were to betray Naruto again in the fanfiction, it would surely make Naruto pissed off. Their relationship is complex and Sasuke's actions have a big impact on Naruto.
It could also be due to the fanfic's poor writing quality. If the grammar and spelling are atrocious and it's hard to follow the story. When it comes to Naruto, fans have high expectations. So, if they can't even understand what's going on with Naruto in the fanfic because of bad writing, it can lead to a 'pissed off' reaction.
Maybe in the fanfiction, Nero has made some decisions that go against Trish's beliefs or values. For example, if Nero decides to trust a character that Trish knows is untrustworthy, it could make her angry.
Maybe he'll go on a rampage in the fanfiction world. He could start using his powerful jutsu to show his anger, like unleashing a Rasengan on the source of his annoyance.
Well, perhaps in this fanfiction, Naruto is somehow involved with the Young Justice team. Maybe they accidentally undermine one of Naruto's important missions or goals. For example, they could interfere in a battle where Naruto was about to achieve something crucial, like rescuing a friend or stopping a powerful enemy. This would surely piss Naruto off as he's very passionate about his friends and his village.
Sasuke could be a possible cause. If Sasuke were to go back on his word about protecting the village or if he were to harm their friends again, Naruto would be pissed. Their relationship is complex, and Sasuke's actions often have a strong impact on Naruto.
A new, powerful and arrogant villain introduced in the fanfic could be the cause. This villain could constantly mock Naruto and his ideals, and try to undermine his efforts to protect the village. Such blatant disrespect would make Naruto really pissed off as he is very protective of his home and the values he stands for.
Maybe Naruto gets pissed off because his friends don't believe in him. For example, if they suspect him of being involved in something bad without evidence.