Preheat oven to 350° F. Line cupcake tin with paper liners.
Combine dark chocolate and cocoa powder in a large bowl. Pour hot coffee over mixture. Cover with plastic wrap and let sit for a couple minutes. Remove cover and whisk until smooth. Chill in the refrigerator for about 10 minutes.
In a medium bowl whisk together flour, sugar, salt, and baking soda.
Once chocolate mixture has cooled, whisk in oil, eggs, vinegar and vanilla. Fold in flour mixture. Divide batter between 12 cupcakes. Remove milk chocolate filling from fridge.
Add a rounded teaspoon of milk chocolate filling on top of each cupcake. Bake for 17-20 minutes until cake is set. Let cool in pan for 3-5 minutes before unmolding and allowing to cool completely on wire racks.