So, first, the issue where NotFound was overriding Home was reported here: https://github.com/dotnet-websharper/core/issues/946 and fixed on master, so it will be corrected in the next release.

Now, this new issue is indeed a problem. The wildcard sitelet on / overrides all URLs, including those that point to files that would otherwise be served by ASP.NET, such as Scripts/*.js. That's not good.

I've experimented a bit, and here is what I've come up with. Essentially, I'm using ASP.NET's error handling to rewrite the URL into one that is handled by our sitelet.

1. In Web.config, add the following:

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   <configuration>
     <system.webServer>
       <httpErrors errorMode="Custom">
         <remove statusCode="404"/>
         <error statusCode="404" responseMode="ExecuteURL" path="/error"/>
       </httpErrors>
     </system.webServer>
   </configuration>

   This will rewrite unrecognized requests to http://your.site.com/foo/bar to http://your.site.com/error?=404;http://your.site.com/foo/bar (not redirect, just rewrite).

2. Recognize the above redirect in the sitelet:

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   type EndPoint =
       // your normal endpoints...
       | [<EndPoint "/error"; Wildcard>] Error of string
   
   [<Website>]
   let Main =
       Application.MultiPage (fun ctx endpoint ->
           match endpoint with
           // your normal endpoints...
           | EndPoint.Error _ ->
               // Parse the original URI from ASP.NET's rewrite, in case you need it
               let requestedUri =
                   let q = ctx.RequestUri.Query
                   let q = q.[q.IndexOf(';') + 1 ..]
                   match System.Uri.TryCreate(q, System.UriKind.Absolute) with
                   // The request was to /error/... directly
                   | false, _ -> ctx.RequestUri
                   // The request was to a non-existent path, and rewritten by ASP.NET
                   | true, uri -> uri
   
               Content.Text (sprintf "Unknown URI: %A" requestedUri)
               |> Content.SetStatus Http.Status.NotFound
       )

I hope this helps!

Side note for anyone else reading this: the above applies when you're using ASP.NET 4.x. If you're using ASP.NET Core or OWIN, then there should not be a need for any of the above: file URLs will correctly be handled first as long as you call UseStaticFiles() before UseWebSharper().