Yeah, currently moving troops through cities and in and out of cities is a real pita.
Iirc Frogboy said it's because cities have set entrances which aren't shown on the cloth map but which are actually used by units.
Anyway, I hope it will get changed soon, since it's one of the things that make the beta unfun atm. (Or perhaps that means they'll leave it in by purpose for a while. 
)
