i know this problem. if you cut faces on polys and extrude alot often large parts are doubled very strange problem i know too.
i think if you work excact when cutting, only hit edges select very carefully, to avoid unwanted backface stuff, and select faces by the small point in the middle only, it doesnt happen so often. but yes i know this problem very strange.
deleting and merging helps yes but i wonder why this happens at all this thing. i have it in maya 5.