The name change to this ticket also suggests that you are discussing a third issue (overwriting of downloaded files when files of the same name are downloaded.)
The bug I am reporting is that a file will be downloaded two times when it shouldn't be. If a folder is selected and a file inside that folder is selected when a download is initiated then the folder and all its contents will be downloaded, as expected, but also the selected file will be downloaded and placed at the top level of the download location. The selected file should not be downloaded two times. It should only be downloaded as part of the contents of the downloaded folder. It should not be downloaded a second time and placed at the top level.
The Finder does all of this in a consistent manner and CyberDuck should do things the same way.
The issue you describe that files are downloaded twice only occurs when dragging the files to the Finder but not when just choosing 'Download' from the Menu. I just observed this. We'll try to fix both issues.