Are they sore all over and are getting hot spots or blisters? I'm not a specialist but the only thing I can think of is the position of your cleats on your shoes and the amount of pressure your applying to your pedaling. If it is a cleat issue, your shoes usually come with a small guide demonstrating where the cleats should go if your getting hotspots or the like. If not, the local bike shop should help you. Hopefully this helps for you!