Preheat oven to 350°F. Line a 12-cup muffin tin with cupcake liners.
In a medium bowl, whisk together the flour, baking powder, cinnamon, nutmeg, and salt. Set aside.
In the bowl of a stand mixer with the paddle attachment, cream butter and sugar.
Add eggs, one at a time, mixing well after each addition.
Mix in vanilla.
Alternating between the flour mixture and milk two times, add each to the creamed butter and sugar, mixing until incorporated.
Divide the batter evenly among the cups of the prepared muffin tin. Top each with about 2 teaspoons of cooled apple filling.
Bake for about 24-26 minutes, or until an inserted toothpick (around the edge) comes out clean.
Let the cupcakes cool for a few minutes, then transfer to a rack to cool completely.