In a medium pot over medium-high heat, combine diced apples, brown sugar, cornstarch, ground cinnamon, and water. Cook until the apples become tender and the mixture thickens, about 10-12 minutes. Remove from heat and allow to cool.

Preheat oven to 350°F (175°C) and line a 12-cup muffin pan with parchment cupcake liners.

In a mixing bowl, whisk together cake flour, baking powder, salt, and ground cinnamon. In a separate bowl, beat the softened unsalted butter until creamy, then add granulated sugar and mix well. Add eggs one at a time, incorporating vanilla extract afterwards.

Gradually add the dry mixture to the wet ingredients, alternating with milk, mixing until just combined. Be careful not to overmix.

Spoon the batter into the prepared muffin liners, filling each about ⅔ full. Bake for 20-22 minutes or until a toothpick inserted in the center comes out clean. Let cool in the pan for 5-10 minutes before transferring to a wire rack.

In a large bowl, beat softened butter and cream cheese until smooth. Gradually add powdered sugar and ground cinnamon until thick and fluffy.

Scoop out the center of each cooled cupcake and fill with apple compote. Top each cupcake with additional compote and frost with cinnamon cream cheese frosting using a piping bag.