I'm running the latest beta version and this is happening to me. Some clips are shown as duplicates, but where they originally appear is NOT shown as a duplicate.
Then in a different scenario - when I have a clip that shows its a duplicate in both instances and I delete the duplicate, the markers dont go away on the original clip. Not sure if its not showing or isnt there or what but its all messed up.
It sometimes updates if you close the sequence and open it back up. But not always.