Something like this happened to me in a multiplayer game and I wasn't using Simultaeous moves, so I don't think it's that. Have you had any crashes due to out of sync errors?
My wife and I were playing multiplayer over our LAN and the game crashed once because of out of sync. When we reloaded there was a sumerian enkidu warrior standing in one of MY cities (we were at peace with sumeria). I couldn't get him out. He wouldn't move for anything. Anytime that city tried to build a unit of any kind, the production box would empty, but no unit would show up (I'd even lose population if I was building a settler or worker). Anytime a unit tried to move into the city it was like they had to fight the enkidu warrior (and the warrior was apparently invincible). If a worker or settler tried to move into the city they just died, if a combat unit tried, it would run the combat, but if my unit won, the enkidu warrior just stayed there at full health. He even upgraded to a pikeman later when the sumerians got better tech. When I eventually went to war with sumeria, that enkidu warrior suddenly took over my city (no battle or anything, the game just let me know). THEN I could finally march a cavalry over there and beat him down. I think I still have the save game if someone would like a screen shot or to see the save file.
