I don't know exactly the reason. But one thing could be: you saved once contacts on your SIM Card and another time on your iPhone. So they are the same and it's now your decision which contact you want to be on your iPhone.
Another thing could be with the Facebook App. Facebook copies your contacts from your friendlist and add them with their name to your adress book on the iPhone.
Just deactivate the access of your contacts to the Facebook App and you have a as clear as adress book on your iPhone.