Make sure that the bolts that attach the cleats aren't coming through the bottom of the shoe and hitting the insole. Just a touch of extra pressure there can be an issue.

Also, it is possible that the shoes just don't fit. The shape of the sole (as in the curvature from side to side) of the shoe can also be causing the issue you are having.

Last possibility that comes to mind is the cleat. Maybe a different pedal/cleat system will fix that pressure point. Personally (and this may or may not be applicable to you), every cleat but Speedplay leaves me with hotspots such as you describe.

Just tossing out some other ideas.