Am I missing something here? As far as I can tell, to enter a city, you just add the special order to "enter structure" to enter a city and (assuming it isn't already occupied by the enemy) your force automatically does so when it arrives (presumably immediately if it isn't travelling anywhere).
But it seems to be random whether it does or not. Usually it doesn't with the order still enacted on the tab.
I've been experimenting with this and there seems no rhyme or reason to it. Sometimes it does. But then I repeat the same move and it doesn't. If they do enter, if they then leave, they won't re-enter.
I've got the latest update.