I have the following media queries in my CSS:
@media screen and (min-width: 0px) and (max-width: 319px) {
body {background-color:red;}
}
@media screen a
You most likely aren't going to be able to fix this. Media Queries are based on viewport size and I imagine IE isn't treating the iFrame as a fully fledged viewport in this context.
Your best bet would most likely be to add a bit of JavaScript that detects the size and adds a class to the at the same thresholds you are using for your responsive design. This would also give you backwards compatibility with browsers that don't support media queries.