Sort for duplicates.
Edit: Also try the Plex Dance, and make sure to follow Plex naming requirements.
Naming and organizing your Movie files
You can add the TMDB/IMDB ID to the folder and file name. That tells Plex exactly which movie to match.
If you want to add info regarding resolution, audio, etc. place it in a single square bracket at the end of the folder/file name.
Example:
/movies
../Avatar (2009) {tmdb-19995} [other.info.here]
..../Avatar (2009) {tmdb-19995} [other.info.here].mkv
