Had the same thing happen to me yesterday after running a sync w/ iTunes. Except... mine made a duplicate of EVERY contact I have. UGH!!! I tried to sync again and it didn't change. I had to go through and delete all the duplicates.
Yes all my contacts are duplicated at least three times each. This is annoying. Anyone have a good solution? I dot want to waste my time deleting each contact to find out it will happen again.