When the Let's Encrypt Certbot tried to validate your domain, it failed to find the IP address (A record) of the domain to match if the certbot is running from the IP location.

Possible Solution 1

Check if the Cloudflare proxy is on for the A record. If it is in on state, turn it off. Usually, this is done by clicking the orange cloud icon on the DNS page for the A record.

Possible Solution 2

If it's already done and still you are facing errors, edit the TTL (Time To Live) field for the A record to 60. Your domain DNS is not propagated and this might speed up the process.

Possible Solution 3

If none of the above works, there is something wrong with the certbot or the connection from the certbot to the DNS of your domain. Add --debug-challenges while you run the command to issue SSL. This might give you more info.

Possible Solution 4

One last resort is to try the manual mode. You can verify the domain ownership via http challenge instead of dns mode. Follow the instructions here in the Certbot documentation.

However, you might need to associate the certificate once issued to your nginx configuration. Find the below config for your reference. You can easily use this make your service / website up and running after getting the certificate.

server {
        server_name example.com;
        location / {
                proxy_pass http://localhost:3000;
                proxy_http_version 1.1;
                proxy_set_header Upgrade $http_upgrade;
                proxy_set_header Connection 'upgrade';
                proxy_set_header Host $host;
                proxy_cache_bypass $http_upgrade;
        }

    listen [::]:443 ssl ipv6only=on; # managed by Certbot
    listen 443 ssl; # managed by Certbot
    ssl_certificate /etc/letsencrypt/live/example.com/fullchain.pem; # managed by Certbot
    ssl_certificate_key /etc/letsencrypt/live/example.com/privkey.pem; # managed by Certbot
    include /etc/letsencrypt/options-ssl-nginx.conf; # managed by Certbot
    ssl_dhparam /etc/letsencrypt/ssl-dhparams.pem; # managed by Certbot

}
server {
    if ($host = example.com) {
        return 301 https://$host$request_uri;
    } # managed by Certbot


        listen 80;
        listen [::]:80;
        server_name example.com;
    return 404; # managed by Certbot

}