Preheat the oven to 350 degrees. Spray a 6-count mini Bundt cake pan with cooking spray.
Remove stems from cherries, dry with paper towels, and chop. Place in a small bowl and toss with 1 tablespoon flour.
In a medium saucepan over high heat, combine the butter and water and cook until the butter melts, stirring occasionally. Stir in 3 tablespoons cocoa powder and let boil for 30 seconds. Remove from the heat.
Combine 1 cup flour with sugar, chili powder, cinnamon, baking soda, salt, and cayenne pepper. Whisk to combine. Add the cocoa mixture, 2 tablespoons cherry liquid, egg, milk, and vanilla. Mix well. Stir the cherries into the batter. Divide evenly among the mini bundt cake pans and bake for 20-25 minutes or until a toothpick inserted into the center comes out clean. Let cool in the pan for 10 minutes.
Place a piece of waxed paper under a cooling rack and invert the cakes onto the cooling rack to finish cooling completely.
To make the glaze, whisk the powdered sugar together with the cocoa powder. Slowly add milk, a little at a time, stirring, until it is a pourable consistency. Stir in the vanilla and drizzle over the cooled cakes.