Sounds like you aren't getting what jonathanm said. You said you had mapped /download, but then you said you expected to find them in /downloads.
/download is not the same as /downloads.
If you had transmission saving into the unmapped folder /downloads then that location would be inside the docker itself, inaccessible from unRAID, and taking up space in the docker.
If this is what you have done, then you should remove the container to clean up that space, then add it back, perhaps mapping /downloads instead of /download.