I noticed that when the unit counts within cities exceed 9 units, that a scroll window appears for the additional units. This can be an issue when you are trying to pick units for a stack that will be leaving the city, as you may not readily be able to see all of the units you are about to group.
This is a minor thing, but I wouldn't mind seeing the City unit window being a 4 wide/3 down configuration (12 total), instead of the 3x3 it is now. We seem to have the screen real estate for it.
