Preheat the oven to 350°F (175°C) and line a cupcake pan with cupcake liners.
In a large mixing bowl, whisk together the flour, baking soda, baking powder, and salt until well combined. Set aside.
In another large bowl, combine the egg, sugar, sour cream, vegetable oil, and vanilla. Whisk until the mixture is smooth and well blended.
In a small bowl or a 2-cup liquid measuring cup, mix the hot coffee and cocoa powder until smooth. Let it sit for 2 minutes, then add this cocoa mixture to the wet ingredients (egg, sour cream, etc.) and stir until fully incorporated.
Gradually add the wet ingredients to the bowl with the dry ingredients and mix until the batter is smooth.
Pour the batter into the prepared cupcake liners, filling each about two-thirds full. Bake for 20 minutes, or until a toothpick inserted into the center of a cupcake comes out clean. Allow the cupcakes to cool completely before filling and frosting.
Once cooled, use a cupcake corer or a paring knife to cut out a 1-inch deep section from the top of each cupcake. Fill each cavity with 1 tablespoon of the cooled cherry filling.