In a mixing bowl, combine crushed graham crackers, dark brown sugar, cinnamon, and melted butter until the mixture resembles wet sand. Line a cupcake tin with cupcake liners and evenly press the crust mixture into the bottoms, using the back of a spoon for a firm base. Set them aside while you prepare the cheesecake filling.

In a large bowl, beat the softened cream cheese with granulated sugar and vanilla bean paste until smooth and creamy, about 2-3 minutes. Once well combined, transfer the mixture to a piping bag fitted with a round tip. Set aside in the refrigerator to chill slightly as you mix the cupcake batter.

In one bowl, whisk together the flour, baking soda, baking powder, spices, and salt, ensuring everything is well incorporated. In another bowl, combine the eggs, light brown sugar, canola oil, and pumpkin purée until the mixture is smooth. Gradually fold the dry ingredients into the wet ingredients, mixing until just combined to retain fluffiness.

Preheat your oven to 350°F (175°C). Fill each cupcake liner halfway with the pumpkin batter, then carefully pipe a generous swirl of cheesecake filling into the center of each cupcake. Top with additional pumpkin batter until each liner is about three-quarters full, ensuring that the cheesecake is nestled within the moist pumpkin mixture.

Place the muffin tin in the preheated oven and bake for 18-22 minutes. The cupcakes are done when they puff up and a toothpick inserted into the center comes out mostly clean with a few moist crumbs. Allow the cupcakes to cool in the pan for 5 minutes before transferring them to a wire rack to cool completely.

While the cupcakes cool, prepare the frosting by beating softened butter until creamy. Gradually add sour cream and vanilla, mixing until fully combined. Slowly incorporate powdered sugar until the mixture is smooth and spreadable, adjusting the consistency if necessary.

Once the cupcakes are completely cool, pipe the frosting generously on top of each cupcake, creating a delightful swirl. For an extra touch, sprinkle crushed graham crackers on top. These cupcakes can be paired perfectly with warm cider, tea, or coffee, making them an ideal treat for your fall gatherings.