For anyone who stumbles on this thread, it looks like the issue was reported 5 months ago,
https://dev.deluge-torrent.org/ticket/3295
So that's that I guess.
And I just checked a development build, 2.1.1.dev7501 and nothings changed, this problem persists.

I tested with a regular torrent file and it works fine however when it opens a plain text file with a magnet link inside it will not set a label, all though it does set the "Move Completed" directory. It will also move the .magnet file to .magnet.invalid even though it loads and starts dow...