Preheat the oven to 350°F. Grease a 24-cup mini muffin pan with non-stick butter spray.
Melt the butter.
Place the graham cracker crumbs and powdered sugar in a medium bowl. Stir them together while gradually adding the melted butter, mixing until it is evenly incorporated.
Divide the graham cracker mixture evenly among all 24 mini muffin cups. Press the mixture firmly over the bottom and up the sides of each cavity to form small crust cups.
Bake the crusts at 350°F for 5 minutes. Remove the pan from the oven and allow the crusts to cool completely.
Finely chop the apples into small pieces. A mini food processor can be used, but stop before the apples become puréed.
In a bowl, combine the chopped apples, sugar, brown sugar, flour, cinnamon, and nutmeg.
Transfer the apple mixture to a baking dish and bake at 375°F for 15 minutes, or until the apples have softened slightly.
Keeping the graham cracker cups in the mini muffin pan, spoon approximately 1 teaspoon or so of the cooked apple mixture into each crust. Sprinkle any remaining graham cracker mixture over the apples.
Return the pan to the oven and bake at 350°F for 5 minutes. Allow the bites to cool completely. Carefully run a knife around the edges to loosen them, then remove them from the muffin pan.
Finish each bite with a drizzle of caramel topping.