if your phone is linked with gmail, yahoo, twitter, facebook, exchange, or any other client... you may have some of those contacts linked. what i would suggest to do is... delete all the accounts from the phone (make sure you do a back up of your contacts first just in case - in contacts, go to menu, import/export, export to sd card or internal)
I have some funky contacts that moved over with my yahoo mail app... they dont show up in my contacts but they do show up in email and for some strange reason in my txt msg app. Im always wiping my phone cuz im always doing something to it. and I know if i just link my primary gmail account. my contact list is perfect... but when i link all my other accounts i get all these crazy contacts (primary emails). Funny thing is if you have emailed someone or they have emailed ya and you still have those email in you inbox the phone will pull them.
Samsung Galaxy S III - Marble White 16GB(Sprint)
Rooted w/ Team Sonic Free GS3 Rom
Recovery: TWRP (FTW!!!)
Nova Launcher Prime user.