Preheat the oven to 350F. In a bowl, mix together the dry ingredients (all-purpose flour, sugar, baking powder, baking soda, salt, pumpkin pie spice, and cinnamon). Set aside.
In another bowl, whisk together the wet ingredients (pumpkin puree, egg, butter, and vanilla extract).
Combine the dry ingredients and the wet ingredients. Stir just until combined.
Grease a muffin pan with non-stick cooking spray or line with paper liners. Divide batter evenly between the 12 muffin liners (they will be about 2/3 full). Set aside.
In a bowl, mix together the softened cream cheese, powdered sugar, flour, and salt.
Using a piping bag or a ziplock bag, fill each muffin with 1-2 tbsp of cream cheese filling. Bake for 15-20 minutes or until a toothpick inserted into the center comes out clean. Remove from the oven and let them cool in the muffin pan for 10 minutes. Enjoy!