Only thing that I can think of is that you might have overlaping vertices. check your model in it's lowest poly form, and if your converting back from sub-d make sure that the setting to convert back to polys are set correctly. Then go back to the area's that you had problems with in sub-d and make sure that there're no duplicated or overlapping vertices. If there are any merge the duplicates together. You might also try selecting the model as an object and try --- polygon------cleanup. that might also help.

good luck