if you have choosen to sync contacts with both iCloud and the computer (Windows/Google/outlook/yahoo) might result duplicate entries. So use singlton sync on all your contacts, calender entries to avoid further inconvienients.
Anyway If it's such annoying to remove them manually,
- sync all your contacts to PC. (i.e: Outlook)
- delete all contact details from your iCloud + Phone
- use 3rd party PC tool to remove duplicates+merge entires via chosed program (i.e Outlook).
- after removing duplicates,re-sync contacts with iTunes as a fresh copy.
- finally, use a singlton sync as iCloud, instead of both local+cloud. otherwise it'll messup again...