Lets encrypt fails with wrong hostname

HI all
Not sure if this is the best place to post, so feel free to move
Iv got a few domains hosted on my server, all using lets encrypt for ssl
Its been a while since I have added a domain to the server, so have had a few updates applied
I recently removed a number of domains and subdomains and went to add a new subdomain.
Created fine, but when I went to generate the ssl it fails with
“ssl.CertificateError: hostname ‘subdomain.websitea.com’ doesn’t match ‘subdomain.websiteb.com’”

I loaded the site and it throws a ssl error saying the cert doesn’t match the hostname either.
Having a look, the domain it is using is the first one on the list, but I havn’t had any issues until now generating certs for multiple domains.

Any ideas whats going on?

Can post full error log for LE if you need it
Thanks in advance,.