I have the same issue and I don't know where they are coming from. I have one cntact with 8 more (that are linked) underneath. I checked my google and there are no duplicates there. The facebook profiles may be causing this, but it is a MESS. I do like the photos from the facebook profiles, so I want to keep them there....not sure how to clean these up either.
If you have the 1.3.1 facebook, it's likely the culprit. I had contacts that had hundreds of duplicates, they manifest themselves as linked contacts.
Log out of facebook, clear the facebook data, and the duplicates will go away. If you log back into facebook set the contact synchronization option to not sync, it should work until they come out with an update.