Preheat the oven to 350 degrees F. Line muffin pans with paper liners and set aside.
In a large bowl, whisk flour, sugar, cocoa powder, baking soda, baking powder, and salt. Add oil, coffee, and eggs. Beat at medium speed with an electric mixer until smooth. Mix in the sour cream and vanilla.
Spoon the batter evenly into prepared muffin cups, filling each 2/3 full. Bake until a tester inserted in center comes out clean, for 16 to 18 minutes. Let them cool in pans on wire racks for 5 minutes. Remove from the pans and cool completely on wire racks.
Spoon Coffee Cream Filling into a squeeze bottle with a long narrow tip. Insert the tip into the top of cupcake and squeeze about 1 tablespoon of filling into center of each cupcake.
Spread the Coffee Butter cream frosting evenly over the cupcakes and garnish with chocolate covered coffee beans, if desired.
Coffee Buttercream Frosting: In a medium bowl, beat the butter at medium speed with an electric mixer until creamy. Gradually add the confectioners' sugar, beating until smooth, then beat in the coffee.