certbot on docker doesn't create multiple live folders for subdomains
For image: certbot/certbot - entrypoint is certbot so you can only include one line certbot arguments.If you want to generate two folders / use --cert-name before you point -w -d for 2nd domain/website2.
command: certonly --email my.name@example.com --agree-tos --no-eff-email --staging --webroot --cert-name website1.example.com -w /var/www/website1 -d website1.example.com --cert-name website2.example.com -w /var/www/website2 -d website2.example.com