Preheat oven to 350°F (180°C) and line a 12 cup muffin tin with cupcake liners.
In a medium bowl, whisk flour, cocoa powder, pumpkin pie spice, baking powder, baking soda, and salt together.
In a large bowl, beat butter and sugar together until lightened and fluffy, about 3 minutes. Add in eggs and vanilla and combine, scraping down the sides of the bowl as needed.
Mix in pumpkin puree, milk, and sour cream. Add the dry ingredients and mix until just combined.
Fill the cupcake liners ¾ full with the cupcake batter. The batter will make 12-15 cupcakes. Bake for 16-18 minutes, or until a toothpick tester comes out clean from the cupcakes. Let cool on a wire rack.
Pumpkin Cream Cheese Frosting
In a large bowl, beat cream cheese and butter together until lightened and fluffy, about 3 minutes.
Place pumpkin puree on a medium plate. Dab the puree with paper towels to remove liquid. I used about 6 paper towels. You will know when it is done, when hardly any liquid transfers to the paper towels. This step is necessary so the frosting won't be too loose.
Add pumpkin puree and pumpkin spice. Mix to combine, and then mix in powdered sugar. Mix in orange gel food colouring.
When cupcakes have cooled completely, pipe frosting on them. I used a Wilton 1M piping tip. Store left overs in the refrigerator for up to 3 days.
Make sure all your ingredients are at room temperature. It helps the cupcakes bake evenly if all the ingredients are at the same temperature.
Mix the cupcake ingredients until just combined. If you stir too long, gluten will form, and the cupcakes will be dense.
Make sure pumpkin puree is dried when using it for the frosting. It will make the frosting too soupy if not dried out enough.
Pipe the frosting on the cupcakes however you like. I used Wilton IM tip.