Ah gotcha, that could be the issue. I feel like Jellyfin should be able to handle that, but the way I have it setup is just placing all my movies in a single movie folder, then Jellyfin takes care of the rest. I then take it a step further and put movies into subfolders alphabetically, so mine would look like

…/jellyfin/movies/S/Star Trek II - The Wratch of Kahn (1982).mkv

This allegedly makes searching faster, but I think you’d need like a couple thousand movies for it to make any difference.

There are times where I don’t really like this, for example Rambo 1 is called First Blood so it’s in the F directory and the rest of the Rambo movies are in the R directory, but Jellyfin will organize it all on the interface so it’s not a huge deal. Edit: you can also make a “Sort Title” so it will live next to the other Rambo’s instead of off by itself with the other F movies.

Also, I think some of my issues are coming from using the TMDB Box Set plugin which automates my collections. I think if you create the collections manually things might go a bit smoother.

Are you organizing the movies by libraries on your drive, or just through Jellyfin? The way I organize things is to have them stored alphabetically on my drive, then move them into collections through the Jellyfin interface. Since Jellyfin is a fork of Emby, (I just use Emby’s folder structure and naming conventions)[https://emby.media/support/articles/Movie-Naming.html] and it works great.

Unfortunately, I’ve found Jellyfin collections to be really finicky and they only work sometimes. There may be a plugin that helps, but I’ve sort of conceded to just not using collections often.

Edit: Jellyfin should also create and populate the collections automatically, and when it works it’s really nice. Looking at my collections they’re mostly all correct, except I’m missing one Rambo movie in my Rambo collection and my Deadpool collection is totally empty, even though I have bother movies. I’ll fiddle around and see if I can fix it if you end up running into the same issue.