iCloud / iOS / Mac Syncing Troubles
To remove duplicate contacts:


  
  Make a copy of your contacts.
  Open Contacts.
  From the Card menu, select Card > Look for Duplicates.
  When asked, click Merge.
  Repeat steps 2 and 3 until no duplicates are found.
  Make another copy of your iCloud Contacts.
  



https://support.apple.com/en-us/HT203565


Then sync those contacts to iCloud. 

Afterwards, turn off contacts on the iPhone in iCloud settings, 
remove all remaining contacts and turn it on again.