So I am new to Emby and was trying it out as an alternative to Plex. I have been using Plex for a couple years. I say this to point out the issue I was having with some files not scanning was not related to the files themselves as my Plex server was able to find the files. It appeared to be the folder/file structure that caused the scanning to skip some of the movies.
This issue seems to be centered around .nfo files created when scanning new library additions.
Example, I have folders separated alphabetically ("Movie">"A-B-C">"A"). Then within that folder, I may have a subfolder for a movie "bundled" with other files related to that movie. (moviename.mp4, moviename.eng.srt, moviename.eng.forced.srt, moviename -trailers.mp4, etc)
In the screenshot below, you can see a folder for the Matrix Collection. Within that there are subfolders for the three movies (each containing the movie and the subtitle files or trailers etc) AND one movie was not in a subfolder (Animatrix).
As you can see in the Emby Search window, the three main films did not scan into the library. I can only assume that Emby saw the Animatrix file as the main movie int eh Matrix Collection folder, scanned and created the nfo file, and then figured the three subfolders were not other movies but some other folders related to the Animatrix movie file. As you can see in the search, I did a search for "Matrix", expected to see four films with word Matrix in the title, and only one film with generated nfo file showed in the results.
I also tested my theory with my James Bond collection (which also had only one file showing in a search). I had all of the series in subfolders within the main James Bond Collection folder; except one additional lone movie file. Emby scanned the one file and skipped all of the other movie subfolders. To fix the problem, I simply created a sub folder for the one lone file, moved it into that folder, and rescanned the library and all of the James Bond movies showed up (Emby created the additional nfo files for each movie within the subfolders).
Thought this might help for those running into the issue as it is a folder structure issue. And maybe a programmer might see this and develop additional code to look in ALL folders within folders.
Hope this makes sense. Happy Scanning
NOTE: The only reason I was creating Folders for movies was if the movie file had an accompanying srt or other special feature files associated with it. If the movie file was by itself, there was no need to create an additional folder. It just hung out in the main "ABC" folder with other orphans until it was matched with a subtitle file or trailer file or special feature file...