Preheat oven to 350°F.
Line a 12-cup muffin tin with paper liners.
Whisk together the flour, baking powder, cinnamon, nutmeg and salt in a medium bowl.
In another bowl beat the sugar and eggs until light and creamy.
While continuing to beat, gradually pour in the butter, then the vanilla. Next add half your flour mixture, then your milk, then remaining flour making sure to beat well after each addition.
Divide the batter evenly among the cups of the prepared muffin tin. Top each with a mound of apple filling.
Bake for about 20-25 minutes or until an inserted toothpick (around the edge) comes out clean.
Let the cupcakes cool in the tin for a few minutes, then transfer to a rack to cool completely.