Gym error

It sounds your GPS drifted you out of range of the gym in the middle of the battle. When this happens, it will let you finish off the pokemon you're currently fighting but then you'll be kicked out and put on lockout for a few minutes.

https://pokemongo.gamepress.gg/gym-errors

I don't know the root cause, but I have seen similar things. I actually get this type of thing a lot in downtown SF, where gyms are constantly under attack, and by a gym near my home. In the latter case, the gym is near a street light that I think interferes with my phone's reception. In the constant attack case, I think there may be some server side issues with too many players accessing a gym. I seldom see any other players, though.

GPS drift at the middle of battle is alright, as normally it only records the "place" when the next battle begins, if you are out of range, you are kicked out, excluding the soft bans.

I agree that this is because of GPS drift. I've had it happen many times, although it hasn't happened for a while now. Unless they've changed how GPS drift works, if you drift out of range of the gym it will soft ban you from battling in that gym for five minutes.