Preheat the oven to 350°F and line a muffin tin with four paper liners.
In a mixing bowl, whisk together the flour, sugar, baking powder, and salt.
Add the softened butter, egg, milk, and vanilla extract to the dry ingredients. Stir until the batter is smooth.
Gently mash half the mixed berries with a fork, then fold the mashed berries and the remaining whole berries into the batter to create a swirled effect.
Divide the batter evenly among the four liners.
Bake for 18 to 20 minutes, until a toothpick inserted in the center comes out clean. Let the cupcakes cool completely.
Spread the cream cheese frosting over each cooled cupcake.