From what you describe it sounds as if Plex is considering both files to be different (quality) versions of the same movie – not 1 movie and 1 related extra. That’s why Plex is even offering you the option to split the files apart.
How exactly did you organize/name your files?
The following two examples should work:
Movies <- the folder linked to your movie library
Movie Name (year)
Movie Name (year).ext
Behind the Scenes
An interesting DVD extra.ext
Movies <- the folder linked to your movie library
Movie Name (year)
Movie Name (year).ext
An interesting DVD extra-behindthescenes.ext
Where .ext is a placeholder for your file extension.
After adding the files properly, you should only need to refresh the movie’s metadata for Plex to pick-up the extra. As the extra is now “known” to Plex as an actual movie, you’ll probably need to perform a full Plex Dance to make it forget and re-add it as an extra anew.
