As far as I'm aware, hay goes brown when exposed to air. It's why hay bales are brown on the outside, but if you break a flake off them then they are green inside. Hay that has gone brown is not necessarily bad for your bunny, I believe it carries slightly less nutritional value than green hay (someone please correct me if I'm wrong).
But unless it's damp and mouldy - and trust me, mouldy hay smells REALLY bad - I don't think there's anything wrong with it.