Weird Behaviour Regarding Series

[TheDreadPirate]

Folder structure does not determine how it is organized in Jellyfin.  Ultimately, the metadata it pulls from IMDB/TVDB/AniDB/etc., determines how it gets organized.  The folder and file names help Jellyfin lookup and match the correct metadata and your folder structure should conform to the link below.

https://jellyfin.org/docs/general/server/media/shows

Additional folder nesting sometimes confuses the metadata lookup.  If you need to have some additional organization, you can do things like adding a show or movie to a "collection" but those show up at the "top level" of the interface and aren't nested in a library.

So there is no way i can just tell it to use the existing structure?

Not that I'm aware of.