Last 2 gym raids all Pokémon fainted just as boss died and I got kicked from gym. Error. Beat boss but no credit. Couldn't renterrenter

Enter the gym, spin the disk. it will let you catch the boss. You just don't get the items.

This usually happens if you are trying to rejoin the fight as the boss is dying. If the boss is really low on HP and there are enough people still in the fight to finish on time, then just wait in the limbo room and heal up your pokemon.