Preheat oven to 350°F (175°C). Line 36 cups of miniature muffin pans and coat with cooking spray.
Using an electric mixer on medium speed, beat the butter and both sugars until creamy. Add the vanilla extract and mix well. Add the egg and beat until blended.
In a separate bowl, combine the flour, baking soda, and salt. Add to the butter mixture, mixing just until combined.
Spoon about 1 & 1/2 teaspoons of the batter into each muffin cup. Bake for 10-12 minutes.
To make the topping:
Using an electric mixer on medium speed, beat the brown sugar, egg, and salt until blended. Stir in the chocolate chips, pecans, and vanilla.
Spoon the topping mixture over each partially baked cupcake. Bake for 8-10 more minutes.