Are you using the “-extra_type” naming or separate subfolders for trailers, deleted scenes, etc?
Do you have each movie in its own folder (along with the extras and/or subfolders)?
Can you provide a directory listing showing how you have the files named and organized?
If you’re running Catalina, see this post and this post about file permissions and external drives. It would seemingly apply to all media, not just extras, but might be worth a double check.
