I've had this problem too. Seems like everything doesnt work as seamlessly as it should. Deleting them didnt work good for me because i found that sometimes they werent exactly duplicates. Sometimes one would have the persons personal email and the other the same persons work email. I found a pretty good trick though that works for me.
Go into "Contacts"
Select contact with a duplicate
Go down and select "Linked Cards"
then select the other duplicate contact
Now the contacts are merged and only show as one contact in your address book.
If your Mac is signed into iCloud (and you have Contacts set to sync), you can go into the Address Book application and use the Card | Look for Duplicates menu bar option.
The only thing I don't like about that is that it tells you the number of duplicates it found, and gives you the option of merging duplicate cards, but it doesn't give you a preview of the data it found.
That being that, the feature has always worked well for me.