MVC 3 System.Web.Optimization Bundles single file
I think you need to add another bundle to it.
For example:
Bundle myJSBundle = new Bundle("~/combined-scripts/custom/my-page", typeof(JsMinify));myJSBundle.AddFile("~/Scripts/Custom/MyPage.js");
Then in your page:
<script src="@Url.Content("~/combined-scripts/custom/my-page")" type="text/javascript"></script>
Reference:- http://www.dotnetexpertguide.com/2011/12/bundling-and-minification-aspnet-mvc4.html
More readings: