Pretty weird/obscure bug here. I am playing a hive mind devouring swarm race, and I had just finished invading the final planet of an enemy empire. However, the empire did not collapse. I thought this was because he still had a sector left, but under the species list it showed the race had 1 pop on 1 planet left, and what was really odd is that planet was in a sector I had already conquered. In the galaxy map this system did NOT show as having an inhabited planet. In the system view it did show as having an inhabited planet. Landing troops on the planet did nothing: they could land, and there was no combat. Also the one inhabitant of the planet did not show as being eaten, but the planet did show that I was occupying it (which shouldn't be possible for my devouring swarm race).
I ended up cancelling the war, and the planet still didn't show as occupied in the galaxy map. However, once I destroyed the starbase in that system the system did swap to the invaded race's control and then the planet showed up normally in the galaxy map.
I ended up cancelling the war, and the planet still didn't show as occupied in the galaxy map. However, once I destroyed the starbase in that system the system did swap to the invaded race's control and then the planet showed up normally in the galaxy map.