You may have overfilled them. Most cupcake recipes require you to fill 3/4 full however these cupcakes get a good rise and the cases should only be 1/2 full of the mixture before they're baked. You might have overbeaten them. Too much air in a cupcake will cause a cupcake to overrise and you will lose the fudgy texture. It's also a good idea to check your oven temperature as if it was too hot the cupcakes can rise rapidly and spill over.