This likely all stems back to the fact that your paths are still not setup per best practice as outlined in the guides. Nothing is a mystery, everything is going somewhere because you have configured one of the components in play to do so. However, having a non-standard setup means it falls to you to understand which parts point to where, instead of just being able to refer to the guides.
When everything is setup correctly, you should not have to manually move nor delete anything. Furthermore, you should not be manually moving or deleting your torrent downloads. You want to make sure that hardlinking is working, otherwise you are going to be failing to seed and/or taking up double the space.
Your categories and paths for your download clients will differ based on the client in use and the path settings within the client in question. I don’t use Transmission but from the brief searching that I did it seems like it is behaving as designed and configured. While it is downloading, it stores partial files in the /incomplete folder. When complete it moves the finished downloads to the /complete folder. By setting a category of tv it will store downloads initiated by Sonarr in the /complete/tv folder. Again, this is not it doing something wrong. This is it doing exactly what it has been configured and told to do.
Once again, I encourage you to fix your paths and setup per the guides. I just remembered that I believe you are running native apps, so paths are less of an issue from a functional standpoint (although /home is still not recommended for the reasons outlined in the guides). However, it is imperative that you understand which piece is pointing to where, which should clear up your ongoing confusion. And possibly consider moving to a torrent client that is covered in the guides, like qbittorrent, if you’re still having difficulty connecting the dots.
