I just discovered (what for me was) a new one...
I was trying to use Yummy to upload some image files into a directory created by a WordPress installation (manual). It wouldn't work. A support ticket to my webhost came back with the explanation that the reason was because the folder I was trying to upload to has the ownership "nobody", instead of my user name.
I suspect this is an issue that is beyond an FTP client's control, but is there anything I can do about this from within Yummy?