Most of the contacts in my Contacts.app are duplicated, but not all. I tried Apple's solution, to no avail.
Contacts that are not duplicated and that have data in Company field, have a column character (;) at the end of what is written in that field.
Adding the column character to an existing duplicated contact does not change anything (whether I add it in one of them or both).
Deleting by hand one of both duplicate contacts erases also the other but only after having quit and come back to the program.
Reimporting the vCard of the hand-deleted contact only recreates it once (even after quitting and coming back to the program).
In iCloud.com, there are no duplicates, neither in my iPhone, nor in my iPad.
I tried exporting as archive the totality of the contacts, erasing them from Contacts.app and reimporting them. But, strangely, the contacts come back, for like a second, and then half the contacts disappear. So instead of having my 808 contacts, only 488 remain and no duplicates (with duplicates there were 1787 contacts).
Mac OS X: El Capitan, 10.11 (15A284) Contacts.app: Version 9.0 (1679)