They more than likely just bought those connectors pre-assembled and in bulk which would explain unused pins.
You can order replacement pins from digi-key here:
http://www.digikey.c...ontacts/1442691 (make sure to pay attention to the minimum quantity you can order)
If you want to try to repair it, you could practice taking out an unused pin to figure the best way to get the broken ones out without damaging the plastic. My guess would be to use needle nose pliers and pull them from the front (where the wires aren't soldered).
Edited by SEgamer, Today, 10:42 PM.