Removing duplicate emails -- What is a dupe?

I ran the "cleanup" folder tool and found purported dupes removed from the target folder and moved to  "Deleted" but they were not what I would call dupes. Rather, the tool removed emails that were also embedded in another email chain -- not what I would call a dupe at all.

Am I doing something wrong?  Is there a tool that will remove dupes that are really two  copies of the same email?

Ken C