Preheat the oven to 350°F (177°C). Grease an 9x9 inch baking pan and line with parchment paper, leaving a slight overhang for easy removal.
In a medium bowl, whisk together the flour, baking powder, baking soda, salt, cinnamon, and nutmeg.
In a large mixing bowl, whisk together the melted butter, brown sugar, and granulated sugar until combined.
Add the eggs, vanilla, sour cream, and milk. Whisk until smooth.
Add the dry ingredients to the wet ingredients and gently stir with a spatula just until combined.
Fold about two-thirds of the cinnamon apples into the cake batter, including some of the juices from the pan.
Spread the batter evenly into the prepared baking pan. Spoon the remaining apples and juices evenly over the top.