I’d recommend applying the “Duplicates” filter to your library to see if they’ve perhaps been merged with other movies (possibly with similar names).
A useful way to help disambiguate movies is to include the release year (in parentheses) after the title:
D:\Videos\Man of Steel (2013).mkv
It’s also possible to include the movie’s ID from The Movie Database or IMDB (in curly braces) as the last part of the file name. See this support article for more information on that (it’s not usually needed except for edge cases):
https://support.plex.tv/articles/naming-and-organizing-your-movie-media-files/
(If you end up changing the file names or paths, be sure to perform the Plex Dance to force redetection.)
