Preheat oven to 400. Line 12 medium sized muffin tins with cupcake/muffin liners and spray lightly with cooking spray. (Will make 12 total muffins)
In a large bowl whisk together flour, brown sugar, cocoa powder, baking soda, and salt. In another bowl whisk together warm water, oil, red wine vinegar, vanilla, egg and egg yolk. Add wet ingredients to dry ingredients and mix until all ingredients are incorporated. Gently stir in chocolate chips, reserving about 2 tablespoons of each kind.
Divide batter evenly between the 12 liners, filling each about 3/4 full. Sprinkle reserved chocolate chips on top of the batter. Bake about 15 minutes until an inserted toothpick comes out clean. Store in airtight container.
Store in airtight container at room temperature up to three days, or in the fridge up to 1 week.