There is a problem with Cyberduck client when dealing with long Filenames and transferring content from a Multi-Directory paths.
This problem has been around for awhile as I'm aware of, and it seems to only relate to Cyberduck as no such problems exist with Transmit 5 client on OSX and CarotDAV on Windows.
For example, when I connect to a Secure WebDAV server I'm greeted by Root folder. There is usually no problems downloading from it. Assuming the file does not have a Longfile name, for example I'm unable to transfer files with 128 Character filename. The transfer fails with Permission Error.
The same can be said for transferring files from Multi-Directory structure path, even if files do not have long names, but the general path is long enough it will also fail with a Permission Error. Ex: WebDAV Server URL/Media/TV_Shows/Show_Name/Season_1/File_Name_S01_E01.mkv