You seem to have successfully obtained a certificate; I guess it just failed to install into Apache, because Apache apparently couldn’t bind to port 443. Do you have something else besides Apache listening on port 443?
sudo lsof -i :443 | grep LISTEN
(Aside: your site seems to be working over HTTPS because it’s behind Cloudflare’s CDN, so I assume you want to use Let’s Encrypt to encrypt the connection from Cloudflare back to your origin server. Of course you can also use Cloudflare’s Origin CA for that, but you would still have to figure out how to install the certificate to Apache anyway.)