Usually when a hero battles against a hero, it`s because of:
- Someone mind controlling a hero or heroes.
- One, both or all of the heroes in question are pulling a hoax on a villain, or villains.
- There has been a misunderstanding (for example, a hero thinks that the other hero has killed someone).
- Someone or something (example: a planet) can only be saved if a hero is killed.
- One/some/all of the heroes have decided to act like villains.
The former has been used in Civil war and Avengers vs. X-men, among others. The heroes usually have a reason to act like villains, in this case. For example, a different political view, saving lifes or a sudden case of insanity. The reason isn`t always good, but it`s a reason.
It`s a typical habit for the heroes to team up for the remainder of the adventure, after the fight ends. Or get scorned at each other.