After updating the Virtualmin > System Settings > Server Templates > Default Settings > Apache Website

The Suexec command on your system is configured to only run scripts under /home, but the Virtualmin virtual server home directory is /var/www/vhosts. CGI and PHP scripts run as domain owners will not be executed.

The solution is to update the first line of the www-data file located at:

/etc/apache2/suexec