Step 1: Make the Pumpkin Batter. Preheat the oven to 350°F and line a 12-cup muffin pan with paper liners. Whisk the flour, sugar, baking powder, baking soda, salt, pumpkin pie spice, and cinnamon together. Add the pumpkin puree, vegetable oil, egg, slightly cooled melted butter, and vanilla. Mix just until combined.
Step 2: Fill the Muffin Cups. Divide the pumpkin batter evenly among the 12 prepared muffin cups, using about ¼ cup per muffin.
Step 3: Add the Cream Cheese and Pepitas. Beat the softened cream cheese, powdered sugar, flour, milk, and salt until smooth. Transfer the filling to a piping bag. Gently insert the tip about ¾ inch into the center of each muffin, then slowly lift it straight up while piping about 1½ tablespoons of filling. Sprinkle the chopped pepitas around the cream cheese.
Step 4: Bake and Cool. Bake at 350°F for 18 minutes, or until the pumpkin portion is set and a toothpick inserted away from the cream cheese comes out clean or with a few moist crumbs. Cool in the pan for 5–10 minutes, then transfer the muffins to a wire rack to cool completely.