Yeah, you need to have both domain names in your cert. Either by using a wildcard or just adjusting your nginx server config and re-running your certbot command.
You should have both names in your server_name like:
server_name atavismxi.com www.atavismxi.com;
Certbot with --nginx would have seen both and asked which names you wanted in your certs. It will still do that once you adjust your nginx config. It will then replace your existing cert.
You may need to fix the server_name in both your server blocks. I am not sure Certbot will do that for you.