Sift the flour, cocoa powder, baking powder, baking soda, nutmeg, and salt into a medium bowl.
In another medium bowl whisk together the butter, yogurt, vanilla, egg, and sugars.
Make a hole in the flour mixture and pour the butter mixture into the hole. Using a rubber spatula, gently stir everything together until there are no more streaks of flour. Mixture will be thick.
Scoop the batter into a piping bag or ziptop bag and snip a small hole in the bottom corner. Squeeze the batter evenly among prepared doughnut tin. Bake for 8 to 10 minutes, or until doughnuts spring back when touched. Let cool completely on a wire rack.
For the frosting:
Place marshmallow fluff in a microwave-safe bowl and heat in microwave until melted and smooth, about 40 seconds. Be careful not to let marshmallow puff over the sides of the bowl when heated. Place graham cracker crumbs in a shallow dish.
Dip one flat side of each doughnut into marshmallow fluff. Place doughnuts on a cooling rack on top of a plate or towel to catch drips. Sprinkle with graham cracker crumbs. Serve.