The Cleanup media tool doesn't actually delete anything unless you tell it to. Once it scans for unused files and duplicates it lists them out for you and you can pick and choose which files you wish to delete or quarantine. A duplicate means one of two things with that tool. Two files with the same hash value (meaning it is EXACTLY the same file) is in two places, or the rough image match thinks they are the same (only applies to images).
That being said, this tool wasn't touched this version and we would appreciate if any concerns/discussion related to this tool could be moved to another thread. This is for the beta release and we want to make sure any genuine reports don't get lost in the back and forth of an unrelated issue.