Maybe there are different expectations among the three. One person wants a more serious relationship while the others just want a casual encounter. So, the one with different views gets kicked out. In a threesome situation, communication is key. If it breaks down, misunderstandings can lead to someone being excluded.
Well, perhaps one person in the threesome realizes they have strong feelings for only one of the other two and their jealousy causes them to act out in a way that leads to them being kicked out.
It could be that in the course of the threesome, one person's behavior becomes unacceptable to the other two. For example, they start making demands that go against the unspoken rules or the comfort levels of the others. This could lead to them being removed from the situation. Threesomes require a certain level of mutual respect and when that is violated, such consequences can occur.
Perhaps Naruto's uncontrollable use of the Nine - Tails' chakra endangers the team during a mission. The village leaders see this as a huge risk and order him to be removed from Team 7. Naruto then embarks on a journey to better control his chakra on his own. He might meet some new friends or mentors along the way who help him become stronger and more in control, and eventually, he tries to make his way back to Team 7.
It could also be due to a false accusation. Perhaps someone framed him for something he didn't do, like stealing important artifacts from the school. And in the world of RWBY, if he was found to be secretly associated with a group that the school considered dangerous, that would also lead to his expulsion.
One possible reason could be a serious rule violation. For example, if Harry was wrongly accused of using dark magic within the Gryffindor common room. Another reason might be that he was framed for stealing the Gryffindor sword. It could also be due to a conflict with other Gryffindor students that got out of hand and the house decided they couldn't keep him anymore.
One possible reason could be his unruly behavior. Naruto is known to be a bit of a troublemaker in the series, always pulling pranks. In fanfiction, this might be exaggerated, and the orphanage might not be able to handle it anymore. Another reason could be that he's suspected of being involved in something dangerous or illegal, even if he's innocent. For example, if there are strange incidents around the orphanage and Naruto is the easy target to blame because of his reputation.
Maybe he was blamed for some trouble he didn't actually cause. For example, if something went missing in the orphanage and the caretakers wrongly thought Naruto took it.
One possible reason could be his prankster nature. Maybe he played one too many harmless but annoying pranks on the staff or other orphans, and they decided they'd had enough. Another reason might be the fear of the Nine - Tails within him. Even if the people in the orphanage didn't fully understand what it was, they could sense something dangerous about Naruto and wanted to distance themselves from him for safety reasons.
There could be a sense of confusion. They may not be sure what they did wrong. And along with that, there might be regret. They might regret getting involved in the threesome in the first place, thinking that if they hadn't, they wouldn't be in this painful situation now. Additionally, they could also feel a sense of relief if the threesome was a situation they were uncomfortable with deep down but didn't realize until they were kicked out.
Maybe he's falsely accused of stealing important Gryffindor artifacts. For instance, if the Sword of Gryffindor goes missing and Harry is wrongly blamed, the house might decide to kick him out. It could be part of a plot by a jealous student or an outside force trying to disrupt Hogwarts.
Tony could become a bit of a rogue figure. Maybe he starts to work against the Avengers at first out of anger and a sense of betrayal. This could lead to some really interesting confrontations between him and his former teammates in the fanfiction.
One reason could be causing disruption. If the 'crusade' involved making a lot of noise, blocking hallways, or disturbing classes, the school would likely take action.