[Agema]

I've seen odd results of this sort, although without indies. I stormed an enemy fort, and my opponent I believe had a stealthy unit that created autospawn that stayed hidden. I took the castle, but found I had lost the province to the autospawn. I've certainly taken forts and been hit by a random province event that has meant my newly victorious army were then besieged in the fort by the event.

I'm guessing that in the OP, with Atlantis breaking siege and you attacking, it resolved like two separate nation's armies invading a third's province (ie. one random attacker verses the defender, and the winner faces the second attacker), the only error being that as your army moved in it reported an empty province.