Pokémon Go: Thrown back to gym menu as soon as countdown ends
Were you at a location where GPS accuracy may have been "suboptimal"? What I experienced often in those cases, is that your location bounces around the area when your GPS updates and decides that you are now in a different location. If this temporary new "wrong" location is too far away from the gym, it may cancel ongoing fights.
In this case, you may sometimes still see the "Gym too far away" message in the gym main menu for a short moment.
This is just a connection issue. Keep trying, or wait a little bit for the servers to calm down and try later.