Rusted iron ore in Travertine?

    I recently remodeled my bathroom in a grey and tan travertine. Some pieces had rust colored spots that I didn't think much of at the time. Until I realized (from water carrying a trail of rust) that it was rust! The owner of the store from which I bought the stone is giving me some bull about it being natural stone, so its not a problem. I understand that the beauty of natural stone is in the flaws, but rust seems more like something I'd find for 50% in a defect pile somewhere. Can anyone tell me if this is normal/acceptable? I'd like the (installed) tiles replaced, but she is offering to seal the tiles instead. Long story short, is rusted metal ore acceptable in travertine, or is this a major defect?

Note: the tiles came from LA Carpet in Las Vegas, NV