In a large mixing bowl, stir together flour, sugar, cocoa powder, baking soda, and salt.
Add in water, oil, apple cider vinegar, and vanilla.
Stir well with a spatula until just combined.
Divide batter among 24 paper lined cupcake tins, about 1/3 full in each cup.
Set cupcake tins aside.
In a separate bowl, place cream cheese, sugar, and egg.
Beat with an electric hand mixer until smooth.
Add in miniature chocolate chips.
Stir with a spoon until chips are combined well with the cream cheese mixture.
Using a tablespoon measure, scoop cream cheese mixture on top of chocolate cake batter in each cupcake tin.
Bake at 350 for 25 - 30 minutes or until a cake tester comes out clean.
Allow to cool completely before serving.
Store tightly covered in the refrigerator.