Sift the flour, sugar, cocoa, baking soda, baking powder, and salt into the bowl and mix until combined.
In another bowl, combine the buttermilk, oil, eggs, and vanilla.
With the mixer on low speed, slowly add the wet ingredients to the dry. With mixer still on low, add the coffee and stir just to combine, scraping the bottom of the bowl with a rubber spatula.
Fold in finely chopped chocolate.
Prepare graham cracker crust. Add melted butter to graham crackers and combine until moistened. Spread about 1 tablespoon of crumbs into bottom of cupcake liner. Press down flat.
Pour the batter (a heaping tablespoon) into the prepared cupcake pans and bake for 18-20 minutes at 350, until a cake tester comes out clean.
Cool in the pans for 30 minutes, then turn them out onto a cooling rack and cool completely.