I find my ankles aching too often after class.
I too have ankle problems... originating from an old soccer injury. A sports doctor explained to me that one of the ligaments healed extended because of improper bracing during recovery thus that extra bit of ligament gets in between the joints causing pain.
I showed him seiza and he says, that thats not the best position you want to put your ankles, injured or otherwise. But if you still want to do it, you crazy aikido ppl, wear ankle wraps and put ice afterwards. Regular massage with curative oils won't hurt either.