This is completely user error here, but I was "secure-deleting" (Finder > Secure Empty Trash) a 2 GB file which takes a while. And during that time I deleted torrents from Transmission (which sends them to Trash) without thinking. I opened Activity Monitor and force quitted the Finder before anything happened but I assume if I didn't know to do that, it would have deleted all my downloads too.
Maybe a nice thing to add would be like the Finder does, not allow you to delete anything from Transmission while the Trash is being emptied:
Hope this made sense…