Destroyed civ coming back to life?

Captured (and thought I destroyed) Samarkand with a size of 1 - window pops up saying I've destroyed the Mongols. Move my unit away from where Samarkand "was" and it's still there, still Brown, and undefended. I can click on the city and view it (as I would be viewing it with a diplomat) and landing back into the city does nothing, in fact my unit blinks on top of the city! Eventually, the dead Mongols manage to build another military unit and I can destroy the city and their civilization a second time. Just another quirk?

Looks like a bug.

It's probably a bug related to the vanishing unit issue that happens sometimes in fortified cities. There's likely still a unit there as far as the game's concerned, but it's not showing. You could probably see it with cived/terraform/jcived. If you successfully defeat a new visible unit in that city while it's still size 1 (as you did), it should be destroyed. Otherwise, it just won't die.

Well, when I conquered the world and got the reply, it said I only defeated the Mongols once.