Step 1: Preheat your oven to 350°F (175°C) and line a standard 12-cup muffin tin with paper liners.
Step 2: In a medium bowl, whisk together the flour, baking powder, baking soda, salt, and pumpkin pie spice until well combined.
Step 3: In a large bowl, cream together the 0.5 cup softened butter, granulated sugar, and 0.5 cup brown sugar until the mixture is light and fluffy.
Step 4: Add the eggs one at a time to the butter mixture, followed by the pumpkin puree and vanilla extract, beating until smooth.
Step 5: Gradually stir the dry ingredients into the wet ingredients until just combined; do not overmix the pumpkin cinnamon roll cupcakes batter.
Step 6: In a small bowl, prepare the cinnamon filling by mixing the 0.25 cup brown sugar, cinnamon, and melted butter.
Step 7: Fill each cupcake liner about two-thirds full with the pumpkin batter. Drop a small teaspoon of the cinnamon mixture on top of each and swirl with a toothpick.
Step 8: Bake for 18-22 minutes, or until a toothpick inserted into the center of the pumpkin cinnamon roll cupcakes comes out clean.
Step 9: While the cupcakes cool, beat together the cream cheese and butter for the frosting until smooth. Gradually add powdered sugar and vanilla, whipping until fluffy.
Step 10: Once the pumpkin cinnamon roll cupcakes are completely cool, frost generously and serve.