I just tried cloning a site and the following message appeared:
Internal Server Error
The server encountered an internal error or misconfiguration and was unable to complete your request.
Please contact the server administrator, and inform them of the time the error occurred, and anything you might have done that may have caused the error.
More information about this error may be available in the server error log.
Additionally, a 404 Not Found error was encountered while trying to use an ErrorDocument to handle the request.
Is it possible that the NS Cloner is not working with the latest version of WordPress (3.6)?