You can block Google from indexing subdomains along with your main account domain with Robots.txt if you wish.
For instance, if you own example1.com and have a subdomain named example2.com that Google has indexed as "example2.example1.com", you can prevent the indexing of such a set of domains.
In the root of /public_html for your main domain example1.com add the following to robots.txt for any add-on domains:
User-agent: *
Disallow: /example2.com
Any additional domains you would add an additional line:
Disallow: /example3.com