Error with certonly mode

That depends which browser I use :wink: - hence asking if you have something which is checking user type - probably to give different content to mobile compared with desktop users.

You may need to add

 <LocationMatch "/.well-known/acme-challenge/*">
        Header set Content-Type "text/plain"
 </LocationMatch>

into your apache config to ensure you just provide a plain text response (since letsencrypt will effectively be using something like curl - and hence getting a 404 error currently).