First thing: EE is asking you to make sure you have your domain or subdomain pointed to your server IP.
Also, make sure www.domain or www.subdomain is also pointing to the same IP. This is basic, if you make a search on forum history you'll find plenty of threads about the same subject.
If you there is no DNS issue then take a look at Let's Encrypt log:
cat /var/log/letsencrypt/letsencrypt.log