NegromancerA wild guess in the dark from me however as to what causes is it would be that the plastic that the shell of the boot is made from is a lot softer than the metal or plastic that the binding is made from. The pressure exerted on the boot from the binding and how the boots toe and heel pieces get pushed around in the binding would probably cause the plastic on the heel and toe to be deformed and gradually be ground down.
The plastic hardness (the "shore" hardness) is normed by the alpine DIN norm and it is softer than the binding. This can sometimes lead to slight chipping, especially on the boot heel since the binding can really slam down in this area.
Small chips are really nothing to worry about, but if you are concerned take them to your local Atomic dealer and have them check it out. They can perform a binding release test just to make sure it is functioning & releasing properly. If it is not and your boot is still within the warranty time period, ask if they can get in contact with Atomic USA and see about fixing/replacing them.