Without knowing the configuration of your kitchen it is hard to judge, but usually the custom cabinetry around a refrigerator is measured to cover it and make it look, as much as possible, as if it were built in. So it usually comes out to just behind the door hinges so there is room to fully open the refrigerator doors. How thick your refrigerator doors are, and where the hinges are placed, should determine the depth of the cabinet for it. Did your cabinetmaker have the refrigerator's detailed specs when doing the measurements for the kitchen? That is the only way to make certain that the cabinet is built to the correct depth for the hinges. Otherwise it is just an approximation.

I agree, it might be negligence from your cabinet designer to inform you about this, but usually if you didn't specify the cabinets to be flushed with the face of the fridge, then that upper cabinets would be the same depth as others. You could ask the company to revise it for you since they didn't inform you properly.