This happens about half the time I play the game now.  Not sure what is causing it.  Sometimes it happens almost right away; other times, after playing a while. You'll notice that the faction borders and city colors don't match and that some cities have randomly changed their names and colors to other city names.   When I click on the city, the correct name appears at the bottom, but not on the map.  The only way to fix this is to either rename the city (to the same name -- though that won't work for the other factions' cities ... you'll see the problem is affecting my neighbor as well) or exiting and restarting; reloading does not fix it.  It didn't seem to happen when I was playing on a small map versus the medium map I am now playing on.