At the battle's start, my lead (ferrothorn) instantly fainted. I had not even chosen my first move yet, so it wasn't a display error. The battle continued as 6 vs 5 until I lost. At this point, the game didnt seem to recognize that I lost and my move timer counted down all the way to 0. The menu options still worked, but I could not switch any pokemon in (including ferrothorn). I was then given a 45 minute ban. Picture is of the battle end when I was forced to let it time out.

Had this happen to me before as well, a good way to prevent this in the future is by healing your pokemon with Nurse Joy before every pvp battle. Even if you win, heal your pokemon. Ever since I started doing that it never happened again.