I have this issue too, and I figured out a workaround. Deleting the files manually via rm frees up space. Deleting files via qBittorrent via UI or automatically does not.
Turns out the files were just being moved to a ".Trash-UID" (where UID is the UID of the container) folder in the /downloads directory (or wherever that folder is mapped to on your host). Clearing that out freed up the space.
I suspect this is a bug where the "Delete files permanently" setting is not being respected. You might want to set up a cron job to delete that folder periodically in the meantime.
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