When no virtual websites are in existence, The Apache web server will point to /var/www/html and /var/www/cgi-bin in a base install of Virtualmin (the default). However when a Virtual website is created, this changes to the first available virtual site, so for example, if the hostname is some.domain.com and no virtual sites are configured, typing this URL in a browser will serve the content in /var/www/html. If a virtual site called virtualsite.com is created, the same request will serve the content of /home/virtualsite/public_html.
By design this is normal
Whilst this is the way Apache is designed and there’s nothing wrong with that, it becomes a problem when some applications are only available outside the virtual server realm (i.e. not suexec’ed). For example the server has Nagios or Munin installed and you want to be able to access it even after a virtual server has been created. The solution is to manually create the first virtual server and call it the same as the server hostname (some.domain.com).