Line a muffin pan with 12 paper liners and set aside.
In a large mixing bowl, whisk together flour, brown sugar, cocoa powder, baking powder, baking soda, and salt. Stir in 1 cup of the chocolate chunks.
In another bowl, whisk together milk, oil, eggs, sour cream, dissolved espresso, vanilla, and vinegar.
Pour wet ingredients into the dry ingredients, stirring just until no dry streaks remain.
Let the batter rest for 20-30 minutes. Meanwhile, preheat the oven to 375°F / 190°C.
Once batter has rested and oven is ready, divide batter equally among muffin cups. They will be very full. Add remaining chocolate chunks on top.
Bake muffins for 15 minutes, or until a toothpick inserted in the center comes out without crumbs. Let cool in the pan 5 minutes before transferring to a wire rack to continue cooling.
If you are making the ganache filling, add the chocolate chips to a microwave-safe bowl and pour the cream over the top. Microwave for 30-40 seconds, then remove and stir until completely melted and smooth. Pour the chocolate into a piping bag or plastic sandwich bag.
Use a smoothie straw, boba straw, or piping tip to remove some of the muffin by poking a hole into the centers. Snip the tip from the piping bag and pipe ganache into each muffin, leaving an extra dollop on top.