Preheat the oven to 375 degrees F (190 degrees C). Butter a 9x13-inch baking dish.
In a large bowl, toss together the apples, pomegranate seeds, brown sugar, cinnamon, and nutmeg. Spread evenly into the prepared pan. In the same bowl, stir together the oats, flour and sugar. Rub in the butter between your fingers until the mixture resembles coarse crumbs. Sprinkle over the top of the fruit.
Bake for 45 minutes in the preheated oven, or until the apples are soft. Let stand 10 minutes before serving. Serve warm or at room temperature.