Preheat your oven to 350°F (175°C). Line a 12-cup cupcake pan with cupcake liners to prevent sticking and make for an easy cleanup.
In a medium bowl, whisk together the all-purpose flour, sugar, baking powder, and salt until well combined.
In a large mixing bowl, beat the room temperature butter with an electric mixer until creamy. Add the sour cream, egg, egg yolks, and vanilla extract. Mix until smooth.
Gradually add the dry ingredients to the wet mixture, mixing on low speed until just combined. Be careful not to overmix.
Fold in the vanilla wafer crumbs gently with a spatula.
Divide the cupcake batter evenly among the lined cupcake cups, filling each about two-thirds full. Bake for 18-20 minutes or until a toothpick inserted comes out clean.
Remove the cupcakes from the oven and let them cool in the pan for about 5 minutes. Then, transfer them to a cooling rack.
In a separate bowl, beat the cream cheese until smooth. Gradually mix in the sweetened condensed milk, whole milk, and vanilla extract, then add the instant vanilla pudding mix and mix until smooth. Gently fold in the diced banana.
Once the cupcakes are completely cool, use a small knife or cupcake corer to remove a small portion from the center of each cupcake. Fill with the banana pudding filling.
Top each filled cupcake with a generous dollop of thawed whipped topping. Garnish with a whole vanilla wafer on top.
