Preheat oven to 350 degrees.
Prepare cake batter according to package directions; fold in apples.
Fill 12 greased or paper-lined jumbo muffin cups three-fourths full. Bake at 350 degrees for 20 minutes or until a toothpick inserted near the center comes out clean. Cool for 10 minutes before removing from pans to wire racks to cool completely.
In a small saucepan, cook the caramels and milk over low heat until smooth. Spread over cupcakes. Sprinkle with pecans. Insert a wooden stick into the center of each cupcake.