Letsencrypt problem: Cannot find domain in the certificate

[AxisNL]

I have a problem when I renew a certificate, letsencrypt doesn't seem to put all names in the cert. If I request a cert for the root domain and a few subdomains I see:

Certificate and Key Saved.
Details
LetsEncrypt request successful for:
ftp.<domain>
mail.<domain>
pop.<domain>
smtp.<domain>
<domain>
www.<domain>
Cannot find domain in the certificate.
However, subdomains have been found instead. Proceeding with them.

And the problem is that the domain name is not in the cert. Any ways to troubleshoot??

 

[AxisNL]

never mind, there was a DNS issue with the root domain (quad a record pointing to wrong ip), but unfortunately the gui does not show those errors. :-/