It’s behaving like it’s pulling those titles from the files’ metadata, but Plex Media Server shouldn’t be doing that with MKV files. What we’d normally suggest for MP4/M4V files is to access Settings -> Agents -> Shows -> TheTVDB (or The Movie Database, if you use that) and moving “Local Media Assets” down in priority (leave it enabled):
After doing that, try performing the Plex Dance on the problem files/directories and see if that helps.
