Perhaps Peter failed to follow Tony's instructions regarding some important technology or protocol. Tony, being a perfectionist and concerned about safety, would then yell at Peter for not listening. In the fanfiction world, this kind of conflict adds drama and tension to their relationship.
Perhaps in the fanfic's storyline, Tony is facing a lot of pressure himself, like threats from powerful villains or issues within the Avengers. Peter's actions, whether they are mistakes or just inconvenient timing, could be the straw that breaks the camel's back for Tony, causing him to yell at Peter.
Peter might be initially shocked and a bit scared. After all, Tony is like a mentor to him. But then he could become defensive, trying to explain his actions or point of view.
There could be a strain in their relationship. Peter might feel hurt and start to distance himself from Tony for a while. However, this could also lead to a deeper understanding between them as they later communicate about their feelings.
Maybe Peter misses an important training session. Tony has probably put a lot of effort into training Peter to be a better superhero. If Peter skips out on training for something unimportant, like going to a party or just being lazy, Tony would be justifiably angry and yell at him for not taking his superhero responsibilities seriously.
One possible reason could be a disagreement over superhero tactics. Peter, being young and idealistic, might yell at Tony if he thought Tony's methods were too extreme or not in line with his own sense of justice. For example, if Tony made a decision during a battle that put civilians at risk, Peter would likely be very vocal about it.
On the other hand, it could also be a turning point for the better. Sometimes a big outburst like that can clear the air. They might realize they've been misunderstanding each other and start to work on their relationship more effectively after the initial shock of the yelling.
Well, it could be that in the fanfiction, they argue about technology. Peter, being the brilliant young mind that he is, might have different ideas on how to use or develop Stark tech compared to Tony. Tony is more experienced and perhaps set in his ways, so when Peter challenges him, an argument ensues.
One possible reason could be jealousy. Maybe Peter has some natural talent or ability that Tony wishes he had, and this makes him mean. For example, if Peter is really good at something like coming up with innovative ideas quickly, and Tony, who is used to being the smartest in the room, feels threatened.
It might be that Tony has some exciting news about a new internship opportunity in the field of engineering. He knows Peter is also interested in that area and calls him during class to tell him all about it and see if he wants to apply together.
Yes, there are many fanfictions with this concept. Writers like to explore the dynamic of Peter being Tony's son as it adds an interesting family - like relationship to the story. It often involves Peter having a closer bond with Tony, getting special training or mentorship from him, and facing various challenges together within the Marvel universe.