Will a Cloned Site Get Indexed Without Links to Inner Pages

I've cloned a site to a new domain just to use the functionality of the site. Everything will be different on the new domain, but there are a lot of left over files and you can access URLs that are identical to the original domain.

Can these URLs, on the new domain, get indexed in Google and cause duplicate content problems? Even if they cannot get indexed, is it best practice to delete them?