If the enemy has an outpost inside the influence of a city and you take the outpost first, when you take and raze the city, the outpost's influence stays distorted by the city's influence even though it's no longer there.  Saving and restarting the game seems to be the only way to fix this.  I had one with influence shaped like a panhead screw and another that only had the square it was located on as influence.  Easy to duplicate.

The AI enemy had a full group of troops on top of a city that was also full.  I attacked the city.  If I tried to attack that group with the group inside the city, only one unit would pop out and attack.  The animation would show the whole group, but only one would end up in the battle.  I was unable to attack this group from outside the city as it would give a stacking error sound like I couldn't pass another group into the city because there was one there.  Duplicating this one requires the AI to stack a group on a city that is already occupied and attacking the city and not the group.