Preheat the oven to 350 degrees. Line 18 muffin cups (you'll need to use 2 muffin tins) with paper cupcakes liners.
In a large bowl combine the flour, apple pie spice, baking soda, baking powder, and salt. Mix well and set aside.
In a medium bowl cream together the butter, sugar, and brown sugar.
Add in the egg and vanilla and mix well.
Stir in the applesauce and sour cream until well combined.
Add the wet ingredients to the dry ingredients an mix until well combined. The batter will be thick at this point.
Fold in the apples. This should make the batter a little bit thinner and easier to stir.
Scoop the batter into the prepared muffin tins so that they are about ¾ full. I use a cookie scoop to do this so there is the same amount in each muffin cup.
Make for 20-23 minutes or until tops are golden brown and a toothpick comes out clean. Cool on a wire rack for 15 minutes.
Meanwhile, to make the glaze put the butter, brown sugar, and milk into a small saucepan. Stir until melted.
Bring the mixture to a boil over medium high heat. Boil for one minute.
Remove from heat and stir in powdered sugar and vanilla.
Allow the glaze to cool for 20 minutes to thicken. Dip the cupcakes into the glaze then place on a wire rack to allow any excess to drip off.