Prep the pan. Preheat oven to 350°F. Line a standard muffin tin with cupcake liners (you’ll get ~18–24 cupcakes).
In a large bowl (or stand mixer), combine eggs, oil, water, sour cream, and vanilla. Mix on medium speed for 1 minute.
Add the cake mix, spice mix, and dry pudding mix. Mix on medium for about 30 seconds, scraping the bowl once. (Avoid overmixing.)
In a small saucepan over medium heat, melt the butter and cook until lightly browned and nutty (1–3 minutes). Add diced apple, brown sugar, cinnamon, and a pinch of salt. Sauté until apples are slightly softened and syrupy, 2–4 minutes. Transfer to a bowl and cool completely.
Add a heaping tablespoon of batter to each liner, spoon ~1 teaspoon cooled apple compote over it (try to keep it centered), then top with more batter until liners are about ⅔ full.Bake 18–22 minutes, or until a toothpick inserted at the edge of a cupcake (not through the compote pocket) comes out clean.
Let cupcakes rest 5 minutes in the pan, then transfer to a rack to cool. Chill briefly in the fridge before frosting if your kitchen is warm.
