A doughy crust can result in several ways, including the dough formulation itself, the size of the pizza and its crust thickness, the type of sauce and amounts of toppings, the way the pizza is baked (e.g., on a pan, stone, screen, etc.), an oven-related problem (e.g., temperature, position in oven, duration of bake, etc.) or a combination of one or more of the above. It may be possible to solve the problem--which BTW is not limited to the whole-wheat pizza--but we would need to have a lot more information to diagnose the problem.
Peter