Line two mini muffin pans with 24 mini muffin cups.
To make the chocolate, microwave the coconut oil for 30 seconds in a small bowl, then stir in the cocoa powder, maple syrup, and salt.
Place a little less than 1 teaspoon of the chocolate at the bottom of each muffin cup—make sure to not use too much and save enough for the top. Put the muffin tin in the freezer until the chocolate solidifies, about 5 minutes.
Meanwhile, make the peanut butter filling. In a small bowl, melt the coconut oil, then stir in the peanut butter, maple syrup, vanilla, and salt until smooth.
Remove muffin pan from the freezer and spoon 1/2 tablespoon of peanut butter filling on top of the chocolate, then cover the peanut butter with the remaining chocolate—1-2 teaspoons. Place a pinch of flake salt on the top, then place peanut butter cups in the freezer until solid—15 minutes, which will give you a gooey peanut butter center, or 30 minutes for a hardened center.
Store the cups in an airtight container in the freezer and enjoy!