As far as I know I've never had this problem prior to this patch (0.912) but I could have just missed it.

Apparently when you move an army though a city it will count as city capacity and not allow you to do so if the units inside the city plus the army would exceed the cities capacity. Depending on the location this can sometimes cause major detours for your army, going around mountains etc.

I just want to be able to move my army -through- the city to the other side without having to take out any units inside the city just to do so.