I really dislike this paradigm that the user needs to become a human DBMS, and rename/link files or write template rules for the media server to understand. It was understandable back in XBMC days but it just feels silly now. Surely it can extract some Musicbrainz-like fingerprint from the media instead of only relying on filename.
But the truly disgusting part is how XBMC/Kodi/Plex/Jellyfin just reassigns the files to another show and there is absolutely no way to audit what's going on other than realizing that some show has two files per episodes or some show you don't have is in the library. Why can't this be easier to inspect?
After two decades I just gave up and use the Home Video mode (just show me my directories mode) on Jellyfin to avoid having to deal with metadata.
For a related issue, Kim Possible was aired out of order, leading to various problems if you watch the episodes in the order they were aired. I am given to understand this is fairly common for older TV shows.
Jellyfin has major problems dealing with this common situation. To Jellyfin, the source of truth is imdb. Imdb numbers Kim Possible episodes in the order they were aired. If you want the metadata that jellyfin scrapes from imdb, and you also want to watch the episodes in an appropriate order, you have to do this:
1. Number all of the episodes in airing order.
2. Ask Jellyfin to fetch the metadata.
3. Renumber the episodes into the correct order.
4. Remember never to ask Jellyfin to scan any directory that contains those episodes again.
If you mess up, Jellyfin will attach descriptions and preview images to every file that aren't, technically, related to the episode in that file.