What if you go to contacts, press menu button, import/export (my phone is not in english so it might not be import and export but anyway) and copy contacts from card to phone memory?
I got instead problem of choosing what contacts to show in contacts on phone (sim, phone, or email accounts and so on). It always shows all contacts, so all phone numbers are duplicated. First it shows from phone memory, then SIM number for same contact.
Sent from my SM-N9005 using XDA Premium HD app