Preheat oven to 350°F (175°C) and grease a muffin tin.
Cut phyllo sheets into squares and layer 3-4 pieces into each muffin cup.
In a bowl, mix pumpkin puree, cream cheese, sugar, pumpkin spice, vanilla, and egg until smooth.
Spoon the mixture into each phyllo cup.
Mix crushed graham crackers, pecans, and melted butter; sprinkle over the cupcakes.
Bake for 18-20 minutes until golden and set.
Let cool and top with whipped cream before serving.