I eventually figured this out using this reddit posthttps://www.reddit.com/r/PleX/comments/iscmne/movie_extras_showing_as_an_extra_as_well_as_a/
Which leads to this forum post
Remove ALL Versions and anything associated with any of these movies from the library - to a ‘Hiding Place’.
Scan Library
Empty Trash
Clean Bundles
You’re not going to like this, but I’m afraid you have no choice. <— As far as I know.
Prepare the first Movie Version with ALL the extras and the movie in the folder (extra folders - I used inline - let’s assume it won’t matter - for now) and put that movie structure in first.
Put ALL the extras in the initial - ‘first version’ folder.
You ca…
tl;dr - Under Settings > Library, turn off “Run a partial scan when changes are detected” then remove the featurettes files from the directory, remove the trash so the movie item is clean, then re-add the featurettes.
