Prep the pans + oven. Preheat the oven to 350°F (177ºC). Line cupcake pans with paper liners.
Mix the dry ingredients. In a medium bowl, whisk together the flour (2 1/4 cups), baking soda (1 1/2 teaspoons), and salt (1/4 teaspoon). Set aside.
Mix the wet ingredients. In another bowl, whisk together the buttermilk (1 cup), vinegar (1 tablespoon), vanilla (1 teaspoon), and eggs (2) until well combined.
Make the cocoa paste. In a small bowl, sift in the cocoa powder (2 tablespoons). Add the red food coloring (1 ounce) and stir until a smooth paste forms. Set aside.
Cream the butter and sugar. In a stand mixer fitted with the paddle attachment, beat the butter (12 tablespoons) and sugar (1 1/2 cups) together on medium speed for about 2 minutes, until light and fluffy. Scrape down the bowl.
Combine the batter.Add 1/3 of the flour mixture and beat on medium speed just until incorporated.Add 1/2 of the buttermilk mixture and beat on low until combined. Scrape down the bowl.Add another 1/3 of the flour mixture and mix on medium until incorporated.Add the remaining buttermilk mixture and mix on low until combined.Add the final 1/3 of the flour mixture and beat on medium just until the batter is smooth. Scrape down the bowl again. Add the cocoa mixture. Add the cocoa–food coloring paste to the batter and beat on medium until fully incorporated. Scrape down the sides and bottom of the bowl, then give the batter a final stir with a rubber spatula to make sure everything is evenly mixed.
Bake. Divide the batter evenly among the cupcake liners, filling each about 2/3 full. Bake for about 20–24 minutes, or until a toothpick inserted in the center comes out clean or with just a few moist crumbs.
Cool. Let cupcakes cool in the pan for about 10 minutes, then transfer to a wire rack to cool completely before frosting. (You can also leave them in the pan, cover, and refrigerate overnight, then frost the next day.)