Special equipment: 2 muffin tins
Make the Fudgy Frosting: Melt the butter in a large saucepan. Stir in the sugar, cocoa, and salt. (It may look grainy or sandy.) In a bowl combine the cream, sour cream and coffee. Whisk into the cocoa mixture and continue heating on low while stirring to dissolve the sugar grains. The mixture should get hot to the touch but never simmer or boil. Remove from the heat and stir in the vanilla. Let cool until it thickens and becomes spreadable, about 3 hours. If too thin, stir in some confectioners' sugar.
Make the Filling: In a standing mixer fitted with a paddle attachment, cream the cream cheese. Add the sugar, egg, and vanilla and blend. Add the chips and mix a few seconds on low to just fold in.
Make the Cupcakes: Preheat the oven to 350 degrees F. In a large bowl, whisk together the dry ingredients. In a large measuring cup combine the water, oil, vinegar, instant coffee, and vanilla. Whisk it into the dry ingredients until just combined and don't worry if there are a few lumps.
Line 2 muffin tins with cupcake papers and fill each 2/3 full of batter. Drop a heaping teaspoon of the filling into the center of each. Bake for 30 to 35 minutes. Cool the cupcakes completely. Frost the cupcakes with the frosting.