Justin –
sorry you are having issues here. no WordPress backup or cloning plugin will support all hosting configurations. The supported platforms are listed here:
https://members.wpacademy.com/wpclone-faq
If you are using one of the supported platforms feel free to post a new support request and then send that link to [email protected].
About destroying two sites — using the plugin is at your own risk for the destination site as is clearly specified in the software. If you are saying the plugin destroyed the source site, that is a very serious issue, please post a ticket to [email protected] with all information possible.
– WP Academy