You only add /tv shows.
Never add any other folder levels – particularly if they are inside the same folder that you already added before.
Keeping the proper folder structure is immensely important when dealing with TV shows in Plex:
https://support.plex.tv/articles/naming-and-organizing-your-tv-show-files/
Failing to do so will get you exactly the kind of issues that you are dealing with now.
Do you have “automatic library scans” activated?
Are the mixed-in episodes in mp4 format, perhaps? If they are, check them for embedded metadata. Or disable “prefer local metadata” in the properties of the library, then perform the Plex Dance with all mixed up shows.
