Charles, the site has been assigned the "OurTheme" stylesheet. It seems that if a site is assigned a stylesheet called "MyStyle", Kentico renders out GetResource.ashx links to every CSS file it finds under /App_Themes/MyStyle. I can't find a straightforward way to disable this behavior.
Brenden, I must have misunderstood you. Yes, "style.css" is in the file system, but I've never seen IIS or ASP.NET behave in the manner you describe. Also, the unwanted
<link> tag's URL is being set specifically to Kentico's GetResources handler.