Yeah that's the Number 1 issue I have with Jellyfin.

It seems to be tolerating whatever semi-organized structure I give it until it just faceplants on some specific show and I have to tediously reorganize the directory structure/names and manual refresh until the metadata lines up correctly.

I like that I don't feel I'm about to be rugpulled on Jellyfin and the client is pretty solid for me but the library scanning is pretty aggravating at times.