I just discovered that I am having a weird issue with Lets Encrypt SSL. I have multiple domains that are configured for domainname.com (without www). I have setup an aliasdomain of www.domainname.com with the parent being domainname.com the www.domainname.com isn't showing in the SSL. Am I setting it up wrong? I have another website which has 2 different domain names. One is long and the other is a shorter version. Website is configured with the long name with www. In the alias domains I list the shorter version with and without www as well as the long version without the www. The SSL is being issues to both the short name domains, but not for the version with the www.
It would be easier to enable auto-subdomain www in the parent website settings. If you really have a reason to use that more complicated method, check also the www domain name points to your server in name service. Then troubleshoot SSL problem with this: https://forum.howtoforge.com/threads/lets-encrypt-error-faq.74179/