I am not sure whether this will answer you.
While you create a folder in your system, it will be sync with the web account, which may take few seconds of time. If you rename or move the folder, whose sync is in process, the sync will be completed with new folder in web and then the second request to rename will be in process, but at the same time, as you have renamed or moved the new folder, the web will sync the desktop version which results in duplication.
When this happens to me often, my practice is to wait for the sync to complete before starting the second task related to the same folder.