Maybe not an issue with hypeDropzone alone. It looks like Elgg itself creates these extra folders. While trying to understand what your problem is I noticed that these extra folders seem to appear on uploading files with the bundled Files plugin (and not only on image uploads but with all kinds of files). I suspect it is connected with the new file upload API introduced in Elgg 2.3. Maybe the upload process does not clean up completely after the work is done.

I've opened an issue about it at https://github.com/Elgg/Elgg/issues/11445.

For what it's worth, the filedrop function used in hypeGallery must be a different method because it saves new icons in the "...<owner_guid>/icons" folder.  I've spent a lot of time comparing the two plugins to discern what's different, but it exhausted my skill set.  Passing 'action' => 'action/gallery/upload/filedrop' to the input/dropzone view allows hypeGallery to control the upload and to put the icons where they should be.