Sgt_Kickaxe - 12:13 am on Apr 23, 2012 (gmt 0)
It's not a google penalty, it's a sign that the wrong page is perceived as your best option for any given search term. This happens a lot when the index page is deemed a stronger page from your site than the article page just because it contains the title and a link to the article but is more established, higher rank etc.
The index page is deemed stronger from your site but it obviously isn't JUST about the topic, there are other articles on the index page too, so it ranks lower. Google doesn't think the index page is explicitly about that keyword set.
Good news, the index page will eventually drop the title/link to that article as you write new articles and your article will rank more highly than the index page did. Some MAJOR sites get around this by changing the link to the article from the index page into an image without alt tag so that the anchor text is not seen on the index page, which means this won't happen.