Prep: Preheat oven to 350°F. Grease 18 muffin cups or line them with paper liners.
Dry Ingredients: In a large mixing bowl, whisk together the flours, oats, baking soda, baking powder, salt, cinnamon, nutmeg, ginger, and cloves.
Wet Ingredients: In a small mixing bowl, whisk together the pumpkin puree, sugar, oil, applesauce, eggs, and vanilla extract.
Combine: Stir wet mixture into dry ingredients, just until combined (do not over mix).
For the Crumble Topping: In a small bowl, use a fork to combine the brown sugar and softened butter until smooth and creamy. Add in the oats and 2 tablespoons flour and stir until topping is crumbly.
Add Topping: Add a heaping 1/4 cup of batter into each muffin tin hole. Sprinkle each muffin with about 2 teaspoons crumble topping.
Bake: Bake in the preheated oven until a toothpick inserted in the center of a muffin comes out clean, about 18-23 minutes (may take longer depending on your pan). To check for doneness, insert a tooth pick and if it comes out clean (except for a few crumbs) then muffins are done.