Assuming we understand you correctly, you are commenting that there is insufficient cover on the top of the pilecap to the pilecap reinforcement should the 2 layer of bars be placed on top of the pile reinforcement.
Usually the assumption is that the reinforcement of the pile need to be reached to the top of the pilecap reinforcement i.e. the pile reinforcement is going in between them. This would be good detailing and construction practice. Not sure whether you have practiced these as all the details have been as such. These have been similarly detailed for the typical pier pile and pilecaps.