Pour the cream for the ganache into a small saucepan and heat it until it’s hot but not boiling, then pour it over the chocolate in a heatproof bowl and let it sit uncovered for 7 minutes before stirring gently until smooth.
If there are a few unmelted chocolate bits, microwave the mixture for 20 seconds, stir again until glossy, and then refrigerate for about 2 hours, or until it’s thick like peanut butter and easy to spread.
Preheat your oven to 180°C (350°F) and line a 12-hole muffin tin with cupcake liners. In a large bowl, whisk together the flour, cocoa powder, baking powder, baking soda, and salt until evenly mixed.
In another bowl, whisk the brown sugar, eggs, oil, milk, vanilla, and vinegar until smooth, then dissolve the coffee granules in hot water and stir that in too.
Pour the wet mixture into the dry ingredients, whisk gently until just combined, and tap the bowl on the counter a few times to release any big air bubbles.
Pour the batter into a jug and fill each cupcake liner halfway, no more, or they’ll overflow and sink later, then bake for about 22 minutes or until a toothpick inserted in the center comes out clean.
Let the cupcakes cool in the pan for 5 minutes, then move them to a wire rack and cool completely for at least 1½ hours before filling.
For the whipped cream filling, beat the softened cream cheese, sugar, and vanilla with an electric mixer for 1 minute until smooth, then add the cream and continue beating until stiff peaks form.
Once the cupcakes are cool, use a small knife to cut out a shallow circle from the center of each cupcake, keeping about a half-inch border, and trim the removed piece into a small lid.
Spoon or pipe the whipped cream into the hole of each cupcake, place the lid back on top, and press gently so it sits flush with the surface.
Spread a generous spoonful of ganache on each cupcake, swirling it over the top, and decorate with chocolate shavings or sprinkles if you like.
Store the cupcakes in the fridge for up to 3 days, and let them sit out for about 30 minutes before serving so the ganache softens and the flavors really shine.