Well the strange thing is it should be not indexed because of the 301. However I found a solution to this:
- First create a disallow and noindex robots.txt; save this in the main wp folder and name it something like robots-subdomains.txt:
User-agent: *
Disallow: /
User-agent: Googlebot
Noindex: /
- In htaccess rewrites of the subdomains to this extra robots.txt file:
RewriteCond %{HTTP_HOST} =subdomain1.example.com
RewriteRule ^robots\.txt$ /robots-subdomains.txt [L]
- Add all subdomains to your google webmaster tools (tools will find the noindex of the robots file and give warning)
- In webmaster tools ask google to delete the url from the index
- Within a few days all false indexed subdomains are gone from google search
