Preheat oven to 350 degrees. Line two standard muffin tins with paper liners; set aside. Whisk together flour, baking soda, cinnamon, nutmeg, and salt in a medium bowl; set aside. Cream butter and sugar on medium-high speed in the bowl of a mixer fitted with the paddle until pale and fluffy, about 5 minutes. Mix in eggs and vanilla.
Reduce speed to low; mix in apples. Add flour mixture; mix, scraping down sides of bowl as needed, until just combined.
Fill lined cups halfway with batter; bake until tops are springy to the touch, 18 to 20 minutes. Remove from tins; let cool on a wire rack. When completely cool, frost cupcakes; top with marzipan apples.
For marzipan apples: Tint some marzipan red and some green (find it in the baking section of your grocery store). Roll red marzipan into balls on a cornstarch-dusted surface. Score bottoms with toothpick. For leaves, flatten teardrop-shaped green marzipan; add veins with toothpick. Roll worms from un-tinted marzipan; add green nonpareils for eyes. Use brown sprinkles for stems. Make holes for worm and stem, and insert.
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