Preheat oven to 350°F and line a muffin tin with cupcake liners.
In a medium bowl, whisk flour, baking powder, baking soda, and salt together.
In a large bowl, beat butter and sugar together until creamy, about 4 minutes.
Add in eggs, one at a time, and mix until each one is combined. Mix in vanilla yogurt and vanilla extract.
Add half the dry ingredients and mix until just combined. Pour in milk and mix, and then add the rest of the dry ingredients. Mix until just combined.
Fill cupcake liners with the batter until ⅔ds full. Bake for 15-18 minutes, or until a toothpick inserted in the center comes out clean.
Allow cupcakes to cool completely before assembly.
Apple Pie Filling
Place apples, water, brown sugar, cinnamon, and nutmeg in a small saucepan. Stir to combine. Add cornstarch and stir to combine.
Heat over medium heat until the filling thickens and the apples soften. Remove from heat and use a potato masher to mash the apple chunks to the size of a pea.
Cool the apple pie filling in the refrigerator until ready to assemble cupcakes.
Preheat oven to 350°F and line a baking sheet with parchment paper.
In a small bowl, whisk flour, sugars, and cinnamon together. Use a fork or pastry cutter to incorporate the butter into the dry ingredients. The butter should be pea sized and well incorporated when done.
Spread the crumbs on the baking sheet and bake for 10-15 minutes. Stir frequently so the crumbs do not bake into a whole piece.
Bake until the crumbs are golden. Remove from oven to a wire rack and stir again. Let it cool down before using.
Store cooled crumble in an airtight container at room temperature.
Caramel cream cheese frosting
Beat cream cheese and butter together until smooth. Add caramel sauce and vanilla extract and beat until combined.
Add in icing sugar and beat until combined.
Core cupcakes with a knife or a cupcake corer.
Carefully spoon apple pie filling into cupcake center. Gently pat it in to get as much filling as possible in.
Use a medium round piping tip to pipe frosting onto cupcakes.
Sprinkle crumble on top of the cupcakes.
Store cupcakes airtight in the refrigerator for up to 5 days.