Just created a subdomain (using add website rather than add subdomain). Can ping website and can get index page if I override the certificate test. It shows that the site is using the host server certificate. The SSL and Letsencrypt buttons automatically untick themselves> I remember having this problem some years ago but can't find the answer.
is it also set to auto create a www subdomain to that subdomain address? i'd assume the dns record for www.subdomain.domain.tld doesn't exist, so it'll fail on that.
This means that Let's Encrypt refused to issue an SSL certificate. Please follow the Let's Encrypt error FAQ to find out why LE does this: https://forum.howtoforge.com/threads/lets-encrypt-error-faq.74179/