Like the title says, many of my shows are putting every episode in just S01. Other seasons are empty. For instance Doctor Who S01 should have 13 episodes, not 99+. This is a new issue, I guess with the recent version update. Here's my typical file structure, which had worked for a long time without this issue.

I just torrent box sets to a folder named for the show typically. I don't use any plugin or other tools to make the files across shows have a consistent file name structure because before, I haven't needed to.

Often, the torrent will provide a top directory that holds all the season directories. I just stick the top one into my more nicely named folder, since I got sick of the badly named torrents in my filesystem.

Any advice? Tips on allowing torrenting to continue while also letting me rename directories to how Jellyfin specifies in the docs?