enemy units apearing in my cities

[THEINFAMOUSPOPS]

Huge world map, LOTS of cities. I start a revolution, and a turn or so later, I relize that there are enemy units in my city! The effect is, when I try to move a friendly unit into a city with enemy units in it, they end up fighting my own units! I tried to play it off hoping it was just an effect of the anarchy and that it would go away, but no... I put alot of time into the game and I'm a little pissed.