Mix flour, sugar, baking powder, baking soda, pumpkin pie spice, and salt in one bowl
In another bowl, combine pumpkin puree and vanilla
Brown butter on medium heat until it turns brown
Add browned butter to wet ingredients and whisk together until cool
Add egg to the mixture
Fold dry ingredients into wet ingredients
In a separate bowl, combine cream cheese, sugar, flour, milk, and vanilla
Transfer cream cheese filling to a piping bag or ziplock bag
Line baking sheets and distribute muffin batter evenly, filling cups about halfway
Poke a hole in the center of each muffin
Pipe cream cheese filling into the holes
Bake at 350°F for 15 minutes
