I runned the plugin yesterday having some issues. Fix them was very simple, checking for resolutions I have not seen something similar in the previous threads so I thought to share my experience and solutions. Just in case someone needs.
Error 524: deactivate completely (delete your site) from the CloudFlare admin panel, wait one or to hours for the change to propagate
Error 500: if the problem is the .htaccess rename the file via FTP i.e. .htaccess_old, then go to the WP admin panel Settings>Permalink and simply click save at the end of the page, a new .htaccess will be created
Error Message : MySQL server has gone away: this is mainly due to the big size of your database + wp-content folders, to fix it it was sufficient to divide the two in this way. If you cannot go back and the screen is completely white in backend and frontend keep calm, open FTP, wp-content>plugins and completely delete the plugin folder: "wp-clone-by-wp-academy". Then re-install it via FTP or by the WP admin panel as you prefer. Try again, if you got again the same error, then do this. In the WP clone advanced settings select the "Back up database only". Then start to create backup. Via FTP copy on your computer the whole wp-content folder of your old site and upload it on your new site replacing the one you already see in the main folder, then follow the last steps provided by the plugin.
I encountered all this issues one by another and always they appear after running the plugin. I think mine was one of the most challenging website.
Hope to be of any help. :-)
It is great!
Thank you guy for this plugin!