When seeing counters increment for Duplicated Policies, this is indicating there are policies with the exact same name, which can cause a conflict within PAN-OS and cause a commit to fail.
The Duplicated Policies do not indicate an overlap or "Shadow" of policies.
The duplicated policy count can be seen in the PROJECT STATISTICS dashboard.
To view the policies with duplicated names you can use the filter by creating a filter for:
POLICIES > Security > FILTER > MERGE > POLICIES > Security Policies > Click the box for Rule Name
Clicking on each case listed in the results will display the policies with the same name in the background. The policies displayed in the backgroud can be edited to change the names.