El Capitan Contacts.app most of contacts are duplicates, but not all
Contact debugging involves the following steps.

Identify source of data. This could be via iTunes sync from a device, a provider like Google, Exchange/Outlook, Yahoo or iCloud or directly in the Contacts app.

Isolate sources causing issues (disable all or one by one if possible).

Identify duplicates and merge. Understand the difference between "link" and "merge" as "link" will not remove duplicates.

If all else fails, use the export option in Contacts to export all contact cards and then re-import the ones of interest. Then you should have a clean setup.