The SiteMap requires that each node must have a unique URL, otherwise it won't be able to differentiate between them when looking up the "current" node. In that case, the first match will always win.
You can work around this limitation by adding an additional query string parameter to the URL.
<mvcSiteMapNode title="Filtered Product" controller="Product" action="Filter" filtered="true"/>
Or by making the request unique by changing the route configuration to include an extra route parameter.
If the URLs are both Internet facing, you can tell search engines that you meant to put the same content on 2 URLs by using the canonicalKey attribute.
<mvcSiteMapNode title="Product" controller="Product" action="Index" key="Product_Index"/>
<mvcSiteMapNode title="Filtered Product" controller="Product" action="Filter" filtered="true" canonicalKey="Product_Index"/>
And then add the canonical HTML helper to the head section of your layout page.
<head>
@Html.MvcSiteMap().CanonicalTag()
</head>
References
http://www.shiningtreasures.com/post/2013/08/10/mvcsitemapprovider-4-seo-features#canonical-tag
https://github.com/maartenba/MvcSiteMapProvider/wiki/Multiple-Navigation-Paths-to-a-Single-Page
https://github.com/maartenba/MvcSiteMapProvider/wiki/HtmlHelper-extensions