tc60045 created the issue

If you happen to be downloading files to a network target (nfs drive, in my case), and that network target is removed, Cyberduck freezes HARD.

You can force quit, but the icon stays in the dock, so it is very strange (I tried ps aux and it wasn't listed, yet it was still there in the dock).

When you formally disconnect (umount or finder eject) the network target (if finder hasn't timed the drive out), then the cyberduck icon in dock disappears.

FYI