As long as the beans are nice and green with no blemishes - enjoy. We always get rust type marks on the leaves (I am not sure that it really is rust) but there is no problem with the beans.

At the end of the growing period of our early broad beans we saw signs of 'Chocolate Spot' which could probably also be referred to as 'rust' but by then most of the beans had been enjoyed. I read that the plants should be destroyed if they get this disease - including the beans - but as Bulbaholic said, he's had no problem with the beans themselves. I think there is a preventive spray against this, but the name escapes me!