Preheat the oven to 350 degrees F (175 degrees C). Line two 12-cup muffin tins with paper liners.
Stir cake mix and Jell-O® mix together in a mixing bowl. Add thawed raspberries with syrup, vegetable oil, hot water, and eggs; beat with an electric mixer until well blended. Pour batter into the prepared muffin cups.
Bake in the preheated oven until tops spring back when lightly pressed, 18 to 20 minutes. Cool in the tins for 5 minutes. Transfer to a wire rack and let cool completely, about 25 more minutes.
Meanwhile prepare mousse filling: Whisk cold milk and pudding mix in a bowl for 2 minutes. Place in the refrigerator until the cupcakes have finished cooling.
Remove pudding from the refrigerator and fold in whipped topping. Load into a pastry bag fitted with a plain pastry tip.
Poke the pastry tip into the center of each cupcake and squeeze until you see the cupcakes expand. Keep refrigerated.