MAKE THE CREAM CHEESE FILLING
Beat together cream cheese, white sugar, vanilla extract, and all purpose flour using the paddle attachment on a stand mixer or use a hand mixer for about 2 minutes until it's smooth. Set aside. Don't beat too much or else it will be too airy and deflate later.
MAKE THE BATTER
Preheat oven to 375°F.
To a large mixing bowl, add all the wet ingredients - white granulated sugar, light brown sugar, eggs, vegetable oil, whole milk, pumpkin puree, and vanilla extract. Whisk until completely smooth.
To the same bowl, add all the dry ingredients - all purpose flour, pumpkin pie spice, cinnamon, baking soda, baking powder, and salt. Whisk vigorously together until you have a smooth batter with no clumps.
Prepare a cupcake tray with liners.
Fill each cupcake/muffin about 2/3 to 3/4 full. Since these are muffins, you want to almost fill it up so that when they bake, you get a signature muffin top look.
Transfer the cream cheese filling to a piping bag with a tip.
Insert the tip into the center of each cupcake and fill it to the top with the filling. Repeat with the rest.
Sprinkle pumpkin seeds around the corners of the muffin.
Bake in the oven for 20 minutes.
Take out of the oven gently and allow it to cool for half and hour before enjoying!