For the cupcakes: Preheat the oven to 350 degrees F. Line 12 muffin tins with paper liners. Whisk the flour, baking soda, nutmeg and salt together in a medium bowl.
Beat the butter and sugar together in a large bowl using an electric mixer on medium-high speed until fluffy, about 3 minutes. Beat in the eggs, one at a time and then the vanilla, beating until smooth. Reduce the mixer speed to low and beat in half the flour mixture until just combined. Then add the sour cream, and then the rest of the flour. Beat until well combined, taking care not to over mix. Stir in the chopped apples.
Divide the batter between prepared muffin tin, filling them 1/2 way full. Bake until a toothpick inserted into the center comes out clean and the tops spring back when pressed gently, about 20 minutes. Cool the cupcakes in the tin on a rack for 10 minutes then remove and cool completely on the rack.
For the frosting: Beat the butter and sugar with an electric mixer on medium-high speed until light and fluffy, 5 to 7 minutes, scraping the sides of the bowl occasionally. Add the marshmallow cream, milk, vanilla and salt and beat on low speed until blended. Increase the mixer speed to high and beat until fluffy and thick, 1 to 2 minutes. Pipe or spread the frosting on the tops of the cupcakes.
When measuring flour, we spoon it into a dry measuring cup and level off the excess. (Scooping directly from the bag compacts the flour, resulting in dry baked goods.)
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