There are many types of these irregularities... I've encountered mostly 'Non-Manifold Geometry'.
Try the cleanup option under mash.
If the result isn't satisfactory(It usually isn't, at least for me) google MEL cleanup scripts. there should be quite a lot.
Welcome to SM :attn:
Hope this helps,
Benny
When in doubt, delete history and freeze transformations.
My latest snake game
(Requires DirectX9 SDK and Framework)