This may due to few reasons.

1. First, your domain resolving methods is important. If you use nameserver methods, you can request SSL certificate for all these domains.
2. But you pointout only the root domain entering A record to DNS server on your domain name registar,  you can request SSL certificate only for root domain.
3. Please check under virtual server details, you enable the SSL for the apache server before request the SSL certificate.
4. It is important to wait about an hours after you point out the domain to the server, because it is take some time to resolve.
5. Better to check it using DNS checking tool before requesting SSL.

I think CyberPanel is far more better than Virtualmin, So try to use it.

Check this Article for more details. https://www.minextuts.com/cyberpanel-install-for-free-web-hosting/