it is not trying to apply a certificate to the domains. It can only find one. I have several being hosted on this droplet

root@PortfolioProjects:~# sudo certbot –nginx
Saving debug log to /var/log/letsencrypt/letsencrypt.log
Plugins selected: Authenticator nginx, Installer nginx
Starting new HTTPS connection (1): acme-v02.api.letsencrypt.org

Which names would you like to activate HTTPS for?

1: ********.com

Select the appropriate numbers separated by commas and/or spaces, or leave input
blank to select all options shown (Enter ‘c’ to cancel):

If using nginx for a django, I found I has used the same upstream for two domains and this caused one not to show up in the certbot list. this was the duplicated code that needed to be unique for each subdomain, had used wwwskorie twice::

  upstream wwwskorie {
       server unix:///home/django/sockets/some_uwsgi.sock ;
  }
  ....
 uwsgi_pass wwwskorie ;
    include /etc/nginx/uwsgi_params ;
 }

Also occurs if you have duplicated server_name