It might be mistaking your virtual path ~/Content/javascripts
for a real path. Try this instead.
bundles.Add(new ScriptBundle("~/bundles/javascripts").Include(
"~/Content/js/custom.js",
"~/Content/js/customizer.js",
"~/Content/js/main.js",
"~/Content/js/bootstrap.js",
"~/Content/js/jquery-ui-min.js",
"~/Content/js/bootstrap-switch-min.js"
));
And in your view.
@Scripts.Render("~/bundles/javascripts")