ssllabs.com test says that there's chain issues (Incorrect order, Extra certs)

This could be an incorrect use of certificates. Make sure to use the following (translate to nginx if you're not using apache)

1SSLCertificateFile /etc/letsencrypt/live/example.com/cert.pem
2SSLCertificateKeyFile /etc/letsencrypt/live/example.com/privkey.pem
3Include /etc/letsencrypt/options-ssl-apache.conf
4SSLCertificateChainFile /etc/letsencrypt/live/example.com/chain.pem

In my case, the issue was on SSLCertificateChainFile. Instead of using "chain.pem", I incorrectly used "fullchain.pem".