I have encountered a related, but slightly different issue. I conquered one of Sumeria's cities - Madrid, since they had initially destroyed the Spanish civilization. At the moment, when I had to decide whether to keep the city, the game suddenly told me that Madrid was Spain's last city and I would get a very heavy penalty for keeping it.
Technically, Civ 6 should not call me the conqueror of Spain at that moment, since it was a random Sumerian settlement, which I took.
(To continue the story I chose liberation in order to avoid the penalty, and guess what: About 2 turns later I got denounced by the revived Spanish civilization.... - but that's a known issue...)