Preheat the oven to 350 F/176 C. With the rack in the middle position. In a large bowl whisk together the flour, unsweetened cocoa powder, salt, and sugar.
Melt the butter in the microwave or in a pot on the stovetop and add it to the dry ingredients and mix with a wooden spoon.
Now, add in the food coloring and then stir, then add in the vinegar. You may need to add more food coloring later on but start with about a tablespoon.
Next, beat the eggs and add those and the vanilla extract into the bowl. Using the wooden spoon, combine all the ingredients together, adding more food coloring at this point as necessary. The brownie batter is done.
In a large bowl add the softened room temp cream cheese and sugar, and cream those together. Next, add the vanilla extract and egg yolk, and mix, scraping the sides as necessary. The cheesecake filling is complete.
Next, place the cheesecake filling into a plastic bag or piping bag,. Once done, twist the bag. Snip off the corner if using a plastic bag.
Take the muffin pan and line it with paper cups or spray with cooking spray. Add some batter, then pipe in some cheesecake filling, then add some more batter on top. Then use a toothpick and twirl it around mixing it. Or just leave it like a sandwich.Bake at 350 F or 176 C for 10 to 12 minutes until when you poke it in the center a toothpick comes out clean.
Now once done, let your brownie bites cool for 5 minutes in the pan before transferring them to a wire rack to cool completely. Enjoy!