The 'Error:MySQL server has gone away' error is a MySQL error

The issue is not specific to WP Cloner. This is a server-specific issue.

1) On shared hosting, this usually indicates that your server lacks resources (memory) to properly handle a MySQL query.

Usually this can be easily addressed by asking your web host to increase your MySQL memory allocation. In any case, you should report the error to your web host. Because they set the server limits, they should be able to resolve your issue easily and quickly.

2) On dedicated server, best is to check MySQL error log file which should point to specific reasons for such errors.

For more information about that error, please visit: http://dev.mysql.com/doc/refman/5.1/en/gone-away.html