First, you should not be showing duplicates of any kind without just cause. This indicates a problem. Where the problem lies hasn’t been determined yet. The most common cause is as I’ve indicated. Adding a directory and then adding its parent in the list of directories for PMS to scan is the most common case here resulting in :facepalm: 
What I am specifically suggesting as first step is :
- Move that file somewhere else. Your home directory / desktop perhaps?
- Perform the Plex Dance
- When you see the episode is now completely gone, move the file back into position where it belongs.
If you find, after updating the library, it still exists, we will have to dig deeper
