A while back when these first came out, some people were making the Deluxe Cheeseburger Salad in them and noticing that the ketchup stained it. HO sent out an email stating that some things will stain them. So, it seems to be a pretty common occurrence (and a silly one if you ask me, especially given the price of these bowls!).
As far as how to get them out, I'm afraid I'm no help.