I have had this same problem so I assume it is a known bug.

Basically you will end with a 'handfull' of enemy infantry left on the top siege tower platform one the main army seems to have run away. I think this happens once the enemy in the seige tower rout maybe.

These 'stuck' infantry just stay still/frozen, whilst you do not seem to be able to move your infantry from the ramparts to the top of the seige tower to kill them.

It is only a minor annoyance really. You can kill them with missle troops or destroy the tower with infantry. Even if you do neither you will still win (assuming you hold the town square). Just speed up the clock to get to the end.