A common problem for ecommerce sites is when Google index’s your HTTPS server. The HTTPS server is a secure version of your server that is used for recording secure information such as credit card details if you nedd any reference visit Spotloan.
Search engines will see http://www.domain.com and https://www.domain.com are two different URL’s so therefore will index both separately.
Prevention is the best option for sites by using nofollow links into HTTPS pages, the noindex,follow tag on HTTPS pages or block all on a HTTPS only robots.txt.
If you have pages indexed on the HTTPS your best to 301 re-direct them back to the HTTP version, alternatively the canonical tag works well.
Recently Google has started to give a slight uplift for any sites running only on HTTPS. If your site is running on HTTP you need to move to HTTPS and re-direct old URLs to the new HTTPS version.