My best guess is that you have previously issued a certificate using the apache plugin on that system, and the renewal config file for that certificate is still there.
$ echo "BreakThisConfig" > /etc/apache2/sites-enabled/000-default.conf
$ ./certbot-auto --apache
2016-05-16 21:33:31,252:ERROR:certbot.le_util:Error while running apache2ctl configtest.
Action 'configtest' failed.
The Apache error log may have more information.
$ ./certbot-auto certonly --standalone -d example.com
- Congratulations! Your certificate and chain have been saved at
/etc/letsencrypt/live/example.com/fullchain.pem.
$ ./certbot-auto renew --force-renewal
Congratulations, all renewals succeeded. The following certs have been renewed:
/etc/letsencrypt/live/example.com/fullchain.pem (success)