Preheat oven to 350 degrees F (175 degrees C). Place muffin liners into two 12-cup muffin tins.
Beat 1/2 cup butter and 1 package cream cheese together in a bowl until creamy and smooth; slowly beat in brown sugar and white sugar until light and fluffy. Add eggs, one at a time, until fully incorporated. Stir in canola oil and applesauce; mix well. Mix in flour, baking soda, baking powder, cinnamon, and salt until just combined. Stir in bananas and 1 teaspoon vanilla extract; fold in pecans. Fill muffin liners 2/3 full with batter.
Bake in the preheated oven until a toothpick inserted in the center of a cupcake comes out clean, 28 to 33 minutes. Cool in the pans for 10 minutes before removing to cool completely on a wire rack.
Beat 1/2 cup butter and 1 package cream cheese together in a bowl until creamy; mix in confectioners' sugar and 2 teaspoons vanilla extract until frosting is smooth. Frost the cooled cupcakes.