Duplicate unrelated files turning up

What folder is this tv show library of yours linked to?
From the screenshot… it should be

/Volumes/Thunderbolt Backup/Videos/English videos/TV/Science & Nature/

However I suppose you’re pointing it to

/Volumes/Thunderbolt Backup/Videos/English videos/TV/

Plex doesn’t like it if you deviate the folder structure from the naming schema.

Library Folder   <- the folder linked to your library...
  TV Show
    Season XX
      TV Show - sXXeYY - optional episode name.ext

Where XX is the 2-digit season number and YY is the 2-digit episode number. Library Folder could be pretty much any name – you can also add multiple library level folders to a single Plex library… however there should be no additional folder levels between that folder(s) and the tv-show folders!

Edit:
After fixing this, you might need to perform a Plex Dance to ensure Plex fully re-scans the episodes: