Line 2 cookie sheets with a silpat baking mat or parchment paper.
Cream butter and both sugars in a stand mixer fitted with the paddle attachment. Mix in vanilla and egg. Add cocoa powder and pudding mix (the powder) and mix until smooth.
Whisk together the flour, baking soda, and salt. Add dry ingredients and coffee or water to the wet ingredients and mix until just combined.
If you are using a stand mixer, add 20 of the mini peanut butter cups and mix until they are broken chunks are throughout the batter. (No need to chop them, the mixer does the work for you.) If you’re using a hand mixer, I suggest quartering the peanut butter cups then adding to the batter and mixing until the chunks are more broken up and spread throughout.
Coarsely chop remaining peanut butter cups.
Scoop 2 tablespoon sized balls of dough onto prepared cookie sheets, 2 inches apart. Press a few pieces of the chopped peanut butter cups on the top of each cookie ball. (This is not mandatory, it just makes them look prettier.) Cover with plastic wrap and chill the cookies sheets for at least 1 hour.
Preheat oven to 350°F. Press each cookie dough ball down slightly with the palm of your hand. Bake for 10-14 minutes, until they just start to lose their glossy sheen. I like mine slightly underdone, so I cooked them for about 11-12 minutes. You might want them to cook a little more. I also like to rotate my cookie sheets in my oven halfway through for even baking.
Cool cookies on cookie sheet for 5 minutes, then transfer to a rack to cool completely. Store in an airtight container for up to 5 days or freeze for up to 3 months.