Make Cream Cheese Filling: Beat together softened cream cheese, granulated sugar, and vanilla extract until smooth. Add milk if too thick.
Mix Dry Ingredients: Whisk together flour, sugar, baking powder, baking soda, pumpkin pie spice, and salt until combined.
Mix Wet Ingredients: Whisk together pumpkin puree, egg, melted butter, and vanilla extract until fully incorporated.
Combine Batter: Fold wet ingredients into dry ingredients until just combined.
Fill Muffin Cups: Divide batter evenly among 12 muffin cups.
Add Filling & Bake: Pipe cream cheese mixture into each muffin, sprinkle with pumpkin seeds and sugar. Bake at 350°F for 18-22 minutes.