I am seeing the same issue.
Thursday, 18-Aug-2016 21:58:07 - mysql query failed. error : 1065 Query was empty - query : ""
In the past, I had relatively zero problem with WP Clone, and I’ve used it multiple times successfully to restore several sites. I was not sure if something on my end has changed regarding the hosting, but seeing that dtmad66 has the exact same issue makes me wonder if it’s the plugin’s problem.