I have successfully used my host’s implementation of Let’s Encrypt for several domains. I tried just now on a new one and it has supplied a certificate for a not-trusted lokacije.ugostitelj.hr by COMODO RSA.
Is this a new problem?
EDIT: I found someone else who has had this problem but received no help: https://www.reddit.com/r/ssl/comments/4wy4xw/why_my_self_signed_ssl_not_working/
EDIT 2: 2 re-issues later, the issue seems to be resolved. Any ideas what happened would still be appreciated.
Looking at the google transparency log - https://www.google.com/transparencyreport/https/ct/?hl=en#domain=laticloud.co.uk&incl_exp=false&incl_sub=true I can see 3 certificates issued, all of which only include your domain and the www. subdomain.
Can you provide the logs / screen dump or more info about where you saw the certificate ? This was a Comodo cert from what you say (so can’t have been issued by Let’s Encrypt). Since both domains seem to point to the same hosting provider, my guess is some sort of miss-configuration at your host
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