Ok, eventually found the problem. This was not a problem with the mime type and I hope this will save someone a few hours. IE9 limits the size of css files to about 250kb, because I'm using bundling and minification one of my css bundles were exceeding this limit and the file was truncated, resulting in some of the styles not being applied.
The fix was rather easy, I split my css bundle into two bundles, for example
bundles.Add(new StyleBundle("~/Bundles/Shared/CSS").Include(
"~/Content/bootstrap/bootstrap.min.css",
"~/Content/font-awesome.min.css",
"~/Content/silviomoreto-bootstrap-select/bootstrap-select.min.css",
"~/Content/kendo/kendo.common.min.css"));
bundles.Add(new StyleBundle("~/Bundles/SharedTwo/CSS").Include(
"~/Content/datepicker/css/datepicker.css",
"~/Content/kendo/kendo.bootstrap.min.css",
"~/Content/bootstrap-touchspin-master/libraries/prettify/prettify.css",
"~/Content/bootstrap-touchspin-master/libraries/prettify/demo.css",
"~/Content/css/Shared/Index.css"));