A SSL certificate provides cover for all your website files and folders, which are included in your hosting space on the same server.
But often a website comprises external files and resources: images, banners, scripts, links to external sites.
In such situations, many browsers correctly display to the user a warning that your website contains both secure and non-secure items (This usually occurs with images, frames, iframes, Flash, and JavaScripts).
This is not a issue of your SSL certificate: it's a issue of your website, and how it's realized.
So, to fix this issue you'll need edit the offending web page and search for http:// references for external images, Flash, iframes, and javascripts. Then change all of them to https://

So, for example

<img src="https://www.externaldomain.com/image.jpg"  />

But this does not work if you are loading contents from another site that does not have SSL set up.