Preheat oven to 350° and spray a 12-cup muffin tin with cooking spray. Prepare cake mix according to package directions.
Divide batter among cups and bake until a toothpick inserted in the center comes out clean, 18 to 22 minutes.
While cupcakes cool, prep pudding and ganache: In a small bowl, combine milk and vanilla pudding mix. Whisk 2 minutes, then let stand until thick, 3 minutes more.
In a small saucepan over low heat, heat heavy cream until it bubbles. Place chocolate chips in a heatproof bowl and pour over hot cream. Let stand 2 minutes, then whisk until smooth.
Let cupcakes cool slightly, then remove from muffin tin and half crosswise.
On cupcake bottoms, spoon vanilla pudding. Top with cupcake tops and spoon over ganache.