Preheat oven to 325 degrees F (165 degrees C). Grease 24 muffins cups or line with paper liners.
Process red apple through a food processor until minced; transfer to a bowl. Process Granny Smith apple through a food processor until minced; transfer to a separate bowl.
Combine cake mix, water, vegetable oil, and eggs in a bowl using an electric mixer or by hand until batter is smooth. Fold 1/2 cup sweet apple and 1/2 cup Granny Smith apples into batter.
Spread graham cracker crumbs onto a piece of waxed paper; add cinnamon and nutmeg. Pour butter over crumbs and mix using your hands until crumbs are moist. Fill each muffin cup with 1 teaspoon crumb mixture and fill the remainder with batter. Sprinkle any remaining crumb mixture over batter.
Bake in the preheated oven until a toothpick inserted in the center comes out clean, 12 to 17 minutes. Cool cupcakes in tin for 5 to 10 minutes before transferring to a wire rack to cool.