mkdir: cannot create directory ‘/var/www/html/.well-known’: File exists
root@65shelbycobra:/home/ubuntu/Downloads/letsencrypt# more /var/www/html/.well-known/acme-challenge/test
12345
That's fine, the other commands should continue to run and you can proceed to test the URL.
Meanwhile, I found this post suggesting it's related to OwnCloud's .htaccess file. A solution is included: