Wrong SSL renew

I have a CWP hosting server with 3-4 accounts. I have a problem with ssl renew every time with a particular domain every time. The main website ssl certificate always come like mail.xyz.com, ftp.xyz.com, webmail.xyz.com intead of xyz.com. When I delete and resinstall ssl certificates, it is ok but there problem in doing this beacuse letsencrypt have limitation so that i cannot delete and renew again. Please show me how to fix this issue. 

Do you have an HTTP -> HTTPS redirect in place for the domain? LetsEncrypt needs to have a working HTTP connection in order to confirm the domain before issuing the certificate.

Is this a subdomain or FQDN?
Is the domain pointing to the servers IP?
Or at the registrar do you have it redirecting to the other domain name?

By default CWP does create SSL for mail, webmail, ftp, cpanel.
Unless you have them unchecked and under Configure you have 'Not renew SAN'