Preheat the oven to 350°F and line a cupcake pan with four paper liners.
In a small bowl, whisk together the flour, cocoa powder, and salt.
In a separate bowl, beat the butter and granulated sugar until light. Add the egg and mix until combined.
Stir in the buttermilk and red food coloring until the batter turns evenly red.
Add the dry ingredients to the wet mixture and stir just until smooth.
In a small cup, combine the baking soda and vinegar, then fold this mixture into the batter.
In another bowl, beat the cream cheese, powdered sugar, and vanilla until smooth.
Spoon a small amount of red velvet batter into each liner. Add a spoonful of cream cheese mixture to the center of each, then cover with the remaining batter.
Bake for 18 to 20 minutes until a toothpick inserted into the cake portion comes out clean.
Cool completely, then dust the tops with additional cocoa powder before serving.