I too had issues where movies found on Plex weren't found by emby. They're listed there (check the listing for the full file name, its probably listed), just the metadata had to be manually identified.
Movies such-as Ant-Man have their file names as "Marvels Ant-Man (2015).mp4" and was listed under "M" without any metadata. If you look up the movie within IMDB, you'll notice the movie is listed as "Ant-Man" and thus the reason it wasn't matched. It's simple to identify the movie and get the proper metadata and images to download.
1) Look the movie up within IMDB.
1.a) E.g. The url for Ant-Man is: https://www.imdb.com/title/tt0478970/
2) Copy the IMDB Movie ID to your clipboard.
2.a) For this example, the ID is tt0478970
3) From the Emby website, find the movie which didn't have it's metadata downloaded, mouse-over it and click the ellipsis (...) and select Identify.
4) Enter the movie name as saved in IMDB ("Ant-Man") as well as the IMDB ID ("tt478970") and click the Search button.
If all goes well, it'll find the movie and update it's metadata and images and you're good to go.
If you have the system configured to save .NFO file to your media directory, you shouldn't have this issue any longer if you ever restore your emby installtion, etc.
Hope this helps..