Preheat oven to 325 degrees. Line a muffin tin with cupcake liners. Recipe makes 24 cupcakes so you may have to cook it in batches unless you have two muffin tins.
Mix together flour, sugar, cocoa, baking soda, baking powder, and salt in a stand mixer using a low speed until combined.
Add eggs, buttermilk, warm water, oil, and vanilla. Beat on a medium speed until smooth. This should take just a couple of minutes. Scrape the sides and bottom of the mixing bowl to make sure everything got mixed in.
Fill each cupcake 2/3 full.
Bake for 20-22 minutes until the cupcakes meet the toothpick test (stick a toothpick in and it comes out clean). Remove from tins and cool completely.
Make the peanut butter cream filling by combining the peanut butter, melted butter, and powdered sugar in a bowl using a hand mixer. Transfer the filling to a pastry bag with a large open tip. Insert the tip into the top of the cooled cupcakes and squeeze about 1 teaspoon of filling into the cupcake. If you inject too much it may split the cake.
Make the frosting by heating the heavy cream in a small saucepan until it just begins to simmer. Pour over the chocolate chips. The heat of the cream will melt the chocolate chips. Let it stand for a couple minutes before stirring, then stir until smooth. Let it cool to room temperature. Using a hand mixer or stand mixer, whip it until it is firm enough to hold a shape. Pipe it onto the cooled and stuffed cupcakes in whatever fashion you think is cute. I just use a plain swirl. Top with crushed pretzel.