Line a baking sheet with parchment paper. Place two-thirds of the milk chocolate chips in a microwave-safe bowl and microwave chocolate for 45 seconds. Stir. If chocolate does not melt completely after stirring, microwave for 20 seconds longer and stir again. Repeat this process until chocolate is just melted.
Place a raspberry in the melted chocolate and use two forks to turn the berry over, coating it on all sides with chocolate. Use a fork to remove the berry from the chocolate, allowing any excess to drizzle back into the bowl. Place the berry on the parchment-lined baking sheet. Repeat this process until 12 berries have been covered in chocolate. Place the berries in the fridge until the chocolate has cooled and solidified, about ½ hour.
Meanwhile, preheat the oven to 350 degrees F. In a large mixing bowl, sift together and combine the following: whole wheat flour, all-purpose flour, cocoa powder, baking soda, baking powder, and salt. In another bowl, whisk together the following: canola oil, yogurt, granulated sugar, egg, and vanilla extract. Slowly add the flour mixture to the oil mixture and stir just until the batter is well combined. Place 12 cupcake liners in a muffin or cupcake pan and fill each liner about half-way with batter. Bake cupcakes about 20 minutes, or until a toothpick inserted in the center of a cupcake comes out clean. Set the cupcakes on the counter to cool completely.
When cupcakes have cooled completely, use a pairing knife or small serrated knife to cut a small hole in the center of each cupcake. Be sure to leave an edge of at least three-quarters of an inch all the way around each cupcake. Also be sure not to cut too far down into the cupcake - an inch of cake should remain at the bottom of each. Slice just the top quarter inch from each round that has been removed from the center of each cupcake to use as a "topper."
Stuff one chocolate covered raspberry in each cupcake. Press the "topper" over the berry, covering up the hole. Cut a fresh raspberry in half lengthwise. Arrange on top of the cupcake, concealing the seams where the "topper" has covered the hole. Melt the remaining milk chocolate chips. Dip a chopstick or kabob skewer or knife edge into the melted chocolate and drizzle all over the top of each cupcake. Serve.
Recipe by Jen Elizabeth's Journals at https://jenelizabethsjournals.com/2013/02/12/sweet-surprise-chocolate-covered-raspberry-stuffed-cupcakes/