1. Check application with 'letsencrypt-auto --version'
2. If no error, try add certificate with 'admin > all > all domains > select one > ssl certificate > add letsencrypt certificate'.
If your domain is domain.com, by default, SAN are 'domain.com,
www.domain.com, cp.domain.com and webmail.domain.com'. So, make sure www, cp and webmail declare in 'A record' for dns setting of domain.com.