After certain events(can't tell witch ones), my teams formation seems to reset to Ryen, Tsubaki, Trey, and Mira. Is there a reason for that?

it doesn't do anything bad you just swap them back

That happens when the party splits and they get later added back into your group. A while ago, I added a system which adds them back into the previous formation, but in some cases it still works by adding them back in order of the database and therefore breaks your formation.