Another posters was cool enough to isolate the reason its inconsistent. If you already have the unit selected it doesn't move to them. If you don't have the unit selected it centers the camera on them correctly. We are working on a fix.
Derek, if I understand you correctly, this is somewhat different. If I'm centered on a unit then click on a city, the screen's focus shifts to it. If I then click on the unit again, it doesn't shift off the city. Instead, the borders of the city are no longer highlighted.
