This is a bug with the Client Copy utility.
This issue is fixed in the following versions:
Automation Engine 12.2.1 – planned release date for October 23, 2018
Automation Engine 12.3.0 – planned release date for February 28, 2019
Deleting and rebuilding the JWP index cache will get rid of all current duplicates; however, running the client copy afterwards will create duplicates again.