Lightly coat twelve 2-1/2-inch muffin cups with cooking spray; set aside. In a large bowl combine all-purpose flour, whole wheat flour, baking powder, pumpkin pie spice, and salt. Make a well in center of flour mixture.
In a medium bowl combine pumpkin, applesauce, egg product, brown sugar, milk, and oil. Add egg mixture all at once to flour mixture. Stir just until moistened (batter should be lumpy). Gently fold in apple and pumpkin seeds.
Spoon batter into the prepared muffin cups, filling each about three-fourths full. Bake in a 375 degree oven for 20 to 25 minutes or until golden and a wooden toothpick inserted in centers comes out clean. Cool in muffin cups on a wire rack for 5 minutes. Remove from muffin cups; serve warm. Makes 12 muffins.