If you add arbitrary subfolders, you better make sure that all the files within are 100% conforming to the Plex naming guide for movies.
https://support.plex.tv/articles/naming-and-organizing-your-movie-media-files/
Otherwise you’ll have to add each subfolder individually to the library.
(does only work if there are no movies in the main folder as well)
Side note: arbitrary subfolders do not work at all for TV show-type libraries.
Filter your library for Duplicates, then inspect the Plex media info of those duplicated items. Chances are that you will find the missing files have been added as versions to existing items, because their file names were too indistinguishable.
There are also a few other things to be avoided in file names: https://support.plex.tv/articles/201381883-special-keyword-file-folder-exclusion/
After fixing the names, you may need to perform the Plex Dance.
