Apparently I have to make a post to fully activate my account so I figured I would be useful and post an answer I figured out to a question I've had for a long time, as I'm sure other people have had the same problem.

I put my siege towers up to the walls and sent my men in up through them. 3/4 worked. one group of units got stuck running around at the base like chickens with their heads chopped off. How I fixed that:

1) Get stupidly angry at it. This will allow you the freedom from rational constraints required to experiment with creative problem solving.
2) Creative problem solving. Order your units to March around at the base of the tower including the sides and back of the tower. Free style it.
3) Miraculously noticed that they are slowly but surely "coming loose" of their attachment to the tower, and that fewer and fewer of them are inside of or directly at the mouth of the tower entrance.
4) When only a couple of them are left attached to the tower, run away from the mouth of the tower. this allowed me to pull my entire unit away from the tower and recommit them to the battle.

Hope it works for you!