f3579a0 created the issue

If you drag something into a Cyberduck window containing only folders and many enough to cover the height of the file list it is not possible to drop into the current folder.
Since the drop area for every folder in the list covers its entire row there is no area that does not hit a folder. A workaround is to back one level and drop it into the folder that way.

I would like to see a drag and drop implementation similar to the Finder where the drop area for a subfolder is constrained to the actual folder data (name, date, size, etc) and the rest targets the current folder.