Sometimes it's difficult to position your army so a free army attacks it in tandem with the garrison. This usually happens when you've already destroyed every free army existent :-D

Never had that problem with falling through the walls, my biggest grouse is about how units in the city can't seem to organise themselves in blocks that block the road no matter how the road twists and turns, but all decide to squash themselves against the walls of one house or other. This especially true for hoplites. Sigh.