Filebot doesn’t dictate the filename. It only renames them to the specifications of the user. By default, Filebot uses the Kodi format. You need to tell it to use the Plex format: Plex naming schemes for FileBot
This is a mis-conclusion. Plex is very tolerant of non-conforming naming schemas. But as your library grows larger, there comes a point where it doesn’t anymore.
If you have issues with mismatches, use a conforming naming schema:
https://support.plex.tv/articles/200220687-naming-series-season-based-tv-shows/
