It seams to have stopped but sometimes the city faction color and symbol was of a different one then mine though it was and had been my city for many turns. This was in 1.05. I am starting a new campaign so I will see with 1.06

ive had wierd things happen after a reload too, like techs dissapearing, units dissapearing, units in training queue to be done in 1-2 turns dissapearing etc. Not to mention 30+ goodie huts magically appearing around my cities on a reload, even when they werent there AFTER i saved the game before