It could be due to a difference in their ideologies. Suppose Tony wants to use a certain unethical method to achieve a goal, like sacrificing some innocent people for the greater good in Peter's view. Peter, being more morally upright, would not stand for it and thus cut ties.
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.
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 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.
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.
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.
A reason could be that Peter is reminded of Tony's last words to him. Those words were full of hope and trust in Peter. When Peter reflects on them, he is overcome with emotion and starts to cry as he feels the weight of Tony's expectations.
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.
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.