Certbot enables root domain, instead only subdomains

Question

I own a domain, lets say example.com.

I want a root domain example.com to be 404 or return a blank page (if 404 is not possible).

sub1.example.com - should redirect a traffic to a running docker container at localhost:3000.

server {
    server_name example.com www.example.com;
    listen 80;
    return 404;
}
server {
    server_name sub1.example.com;
location / {
    proxy_pass http://localhost:8000;
    proxy_set_header Host $host;
    proxy_set_header X-Real-IP $remote_addr;
    proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
    proxy_set_header X-Forwarded-Proto $scheme;
}

}

Everything works fine, until I do a sudo certbot to generate a certificates (with letsencrypt) and install them + redirect http to https.

In activation process I do only for sub.example.com:

server {
    server_name example.com www.example.com;
    listen 80;
    return 404;
}
server {
    server_name sub1.example.com;
location / {
    proxy_pass http://localhost:8000;
    proxy_set_header Host $host;
    proxy_set_header X-Real-IP $remote_addr;
    proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
    proxy_set_header X-Forwarded-Proto $scheme;
}


listen 443 ssl; # managed by Certbot
ssl_certificate /etc/letsencrypt/live/sub1.example.com-0002/fullchain.pem; # managed by Certbot
ssl_certificate_key /etc/letsencrypt/live/sub1.example.com-0002/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 ($host = sub1.example.com) {
        return 301 https://$host$request_uri;
    } # managed by Certbot
server_name sub1.example.com;
listen 80;
return 404; # managed by Certbot



}

Now sub1.example.com works fine, but it somehow redirects root domain example.com to the same docker container running at localhost:8000.

Did I miss something ?

sub1.example.com -> should work example.com -> should not work