I flash android ROM pretty often and contact synchronization always happened and it might mess up when synchronization is duplicated. I’m not sure whether you have this similar problem as mine but I think this tutorial should be good for those who has duplicated contacts now in their phone. Check out the simple tutorial below. I got it done. It is great!!

1. Firstly, log into Gmail account.
2. Select Contacts at the left top corner. 
3. Select More -> Find & merge duplicates. 
4. Your duplicated contacts will be found. Press Merge to continue.
5. The contacts were merged successfully. 
6. Check your contact now and you should see all the duplicated contacts are removed and synchronized.