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.
One possible reason could be a misunderstanding. Maybe Peter accidentally gets involved in something that looks bad to the Avengers, like being in the wrong place at the wrong time during a security breach. So they misjudge him and are mean as a result.
Maybe Peter discovers that Tony has been keeping secrets from him that directly affect his life or safety. For example, if Tony has been secretly monitoring Peter without his knowledge, Peter might feel betrayed and cut ties.
It could also be due to external pressure. The media or some powerful figures in the fanfiction world might force Tony to stay away from Peter. They could spread false rumors about their relationship or use their influence to separate them for their own gain.
One possible reason could be that Tony sees a lot of potential in Peter. In the original story, Peter has great powers and a good heart. The fanfiction might explore different scenarios of their relationship, like a mentor - mentee relationship in more depth. Tony might be interested in how fans envision their interactions and the growth of Peter under his influence.
Peter could stand up to Tony. By showing his strength and not taking Tony's meanness lying down, he might earn Tony's respect. For instance, if Tony makes a snide comment, Peter could give a smart comeback that makes Tony see him in a new light.
One possible reason could be a misunderstanding. Maybe Peter overheard something Tony said and misinterpreted it as a sign of mistrust or dislike. For example, if Tony was talking to another character about Peter's abilities in a way that Peter thought was critical rather than constructive.
One possible reason could be that Tony Stark is being overly critical of Peter's superhero work. Maybe Peter made a big mistake during a mission, and Tony's harsh words in his attempt to correct Peter made him cry. For example, if Peter accidentally put civilians in danger and Tony scolded him severely.
Another reason could be jealousy. In some fanfictions, Tony might be jealous of Peter's natural abilities and the way he is so quickly embraced by the public. Peter, in turn, could be envious of Tony's resources and experience. These emotions can fuel arguments between them. Their relationship is complex and full of potential sources of conflict like this.
It could be that Peter was in a hurry and didn't have time to talk. He might have been in the middle of something important in his own life, like dealing with school or helping a friend, and just had to end the call abruptly.
One possible reason could be that Peter might feel like he's a burden to Tony. Maybe he made a big mistake and is afraid of Tony's reaction. For example, if he accidentally endangered the lives of others during a mission while under Tony's supervision.