If I run a SSL check on SSL Labs it show the main sever using 2 certificates and the second being a mismatch at it is using one from another domain on the server.
https://www.ssllabs.com/ssltest/analyze.html?d=snapto.co.uk&hideResults=on
A problem is that for other domains sub domains in a browser using https://subdomain.com it shows as insecure because it says it is using this second certificate.
If I load the main servers website clicking the lock icon shows the correct details.
I use Cerbot and in httpd conf point to the letscrypt certs in /etc/ i.e.
SSLCertificateFile /etc/letsencrypt/live/snapto.co.uk/cert.pem
SSLCertificateKeyFile /etc/letsencrypt/live/snapto.co.uk/privkey.pem
SSLCACertificateFile /etc/letsencrypt/live/snapto.co.uk/fullchain.pem
I worked out that it was the order of the sites in httpd.conf which was the reason for the other domain showing as for a second certificate so I moved the main server's SSL's listing to just beneath it's none SSL listing.
The issue with other domains which have aliases if using https remains.