Google is indexing top level domain content as though it belongs on subdomains and I want to disable this.

My site has wildcards enabled and we also have two subdomains with unique content. The first subdomain serves as a blog, the second one has only one page. Both have backlinks. Google has indexed content from the main site under the subdomains as well.

Let's say that we have a page at example.com/page.html . The same page has also been indexed as subdomain.example.com/page.html as well and sometimes ranks better than the one located at the main site.

The thing is that we never placed this content at the subdomain. I've thought about adding canonical tags at the subdomains to help with the duplicate content issue.

How can I stop Google from indexing those pages? I don't even know how Google found those, since we never placed them at the subdomains.