I AM not wrong, there are issue with Let's Encrypt. If you have a website with HTACCESS and Extra Apache configuration Let's Encrypt can be unable to issue the certificate so you need remove HTACCESS and Extra Apache Configuration than issue the certificate and put back again HTACCESS and Extra Apache configuration.
You may have issue also in the auto renew after 3 month because as Let's Encrypt have issue on creating the certificate I think the same issue will be present on renew so website will go down and not work than you need every 3 month reissue the certificate after removed Apache extra configuration and HTACCESS.