First, make the truffles. These will take a couple of hours to chill in the fridge so make them first. In a small saucepan over medium heat, bring the crème fraîche to a boil, whisking constantly. Once it starts to boil, remove from heat immediately and add in the chopped chocolate. Stir the mixture with a spatula until all the chocolate has melted and the mixture is homogeneous. Add the butter and continue to stir until fully combined and glossy. Pour the truffle mixture into a bowl, cover with plastic wrap, and refrigerate for 2+ hours or until completely set.
Then, roll the truffles. Remove the bowl from fridge to warm slightly for 5-10 minutes. Line a baking sheet or plate/tray with parchment paper and set aside. Using a melon baller or a small spoon, scoop out and roll 1-inch chocolate truffles with your hands (working quickly so that chocolate doesn't melt). Place on tray and pop in the freezer for 5-10 minutes to firm up again. Then toss truffles cocoa powder to coat (this step is optional!). Then set aside while you make the cupcakes.
Make the cupcakes! Preheat the oven to 350° F and grease two 12-cupcake pans with either butter or cooking spray, or line with paper cupcake cups. In a medium bowl, sift together all of the dry cupcake ingredients (flour, sugar, cocoa powder, baking soda, baking powder, salt), and whisk to combine.
In a separate large bowl, whisk together the eggs, sour cream, canola oil, and vanilla extract until fully blended and creamy. Once combined, add in the dry ingredients and use a spatula or wooden spoon to mix. Fun step! Poor in that cup of piping hot coffee and stir until fully combined (it’ll take some working). Pour batter into the cupcake pans (each one should be about 2/3-3/4 full) and bake for 17-22 minutes or until a toothpick inserted into the middle of one of the cupcakes comes out clean. Remove from oven and let cool.
While the cupcakes are cooling, make the buttercream! In a large bowl, using an electric mixer, beat the room temp butter until creamy. Add in the powdered sugar 1/2 cup at a time and beat on low until combined. Then add in the cocoa powder, vanilla, and salt and continue to beat on medium high until fully smooth, and combined. Either use a spatula to spoon the frosting into a piping bag or simply frost each cupcake using a spoon or knife – however fancy you want to get.
Before frosting, and once the cupcakes are cool, use a small paring knife to cut a 1×1 inch square in the top of each cupcake and take that chunk of cake out (should be a small cube). In the hole, add one of the prepared truffles and press down slightly (don't worry about it looking great, it'll be covered in frosting!). Once all cupcakes have been filled with truffles, frost them with a piping bag or a butter knife, then serve!