Is ‘debug’ logging activated on the server?
Scanning only one library as opposed to all libraries makes it easier to find relevant stuff. Your best bet are the Plex Media Scanner.log files. They should at least contain a line that says something like: “Nothing has changed in M:\Movies-X, skipping folder”.
Your best bet would be to use ExportTools and then filter this for the file name(s) in question.
If the file names are present, you can assume that the file is seen by Plex but was mismatched.
If the file names are not present, they might indeed have been ignored, caused by either their file names, their access permissions or by some forgotten .plexignore file.
I’ve collected a few things to check in this post: How to find the discrepancy between number of files on disk and the number of movies in the Plex movie library
