Could not see the forest for the trees
This is a good lesson learned, actually.
I bet all the attention was going into getting the encryption routines exactly right and nobody checked to see they were being called at all in every case they were required.
I've had oversights like that myself (not on such a high profile product, thankfully), but this is a good reminder to take a step back now and again and take a panoramic look at what I'm doing.