Preheat the oven to 350 degrees and line a 12-count muffin pan with cupcake liners. Set aside.
Red Velvet Cupcakes: Whisk together the flour, sifted cocoa powder, baking soda, and salt in a medium-sized bowl. Set aside.
In the bowl of an electric stand mixer (or handheld) using the paddle attachment, beat the butter on med-high until smooth and creamy. Add the sugar and beat for about 1 minute on med-high speed (will be crumb-like). Add the egg, vegetable oil, red gel food coloring, vanilla extract, and vinegar and mix at low speed until combined. You may need to scrape the sides of the bowl a few times.
Add about half of the flour mixture and mix at low speed until almost incorporated (about 5-10 seconds). Then mix in the buttermilk until almost combined. Finally, mix in the rest of the flour mixture. Remove the bowl from the stand mixer and use a silicone spatula to fold the rest of the batter together (the batter should be mostly smooth and slightly thin).
Fill the cupcake liners 2/3 of the way full (about 3 tbsp of batter, I use my cookie scoop) and bake for 15-18 minutes, or until a toothpick inserted into the middle of the cupcake comes out clean. Allow them to cool in the pan for 5 minutes and then transfer them over to a wire rack to finish cooling.
Cream Cheese Frosting: In the bowl of an electric stand mixer (or a handheld) using the paddle attachment, beat the cream cheese and butter on high speed until combined and creamy (about 2 minutes). Add the powdered sugar and vanilla extract and beat on low speed for about 30 seconds. Increase the speed to medium-high and beat for an additional 1-2 minutes until smooth and creamy.
Frost the cooled cupcakes. I placed the cream cheese frosting in a piping bag and used the Wilton 1A piping tip. Store leftover cupcakes in an airtight container in the refrigerator for up to 5 days.