Preheat the oven to 400 F. Lightly coat a 9-inch square baking dish with cooking spray.
In a large bowl, add the apple slices. Sprinkle with lemon juice.
In small bowl, combine the sugar, cornstarch and cinnamon. Add the mixture to the apples and toss gently to mix. Stir in the blueberries. Spread the apple-blueberry mixture evenly in the prepared baking dish. Set aside.
In another large bowl, combine the flours, sugar, baking powder and salt. Using a fork, cut the cold margarine into the dry ingredients until the mixture resembles coarse crumbs. Add the milk and vanilla. Stir just until a moist dough forms.
Turn the dough onto a generously floured work surface and, with floured hands, knead gently 6 to 8 times until the dough is smooth and manageable. Using a rolling pin, roll the dough into a rectangle 1/2-inch thick. Use a cookie cutter to cut out shapes. Cut close together for a minimum of scraps. Gather the scraps and roll out to make more cuts.
Place the dough pieces over the apple-blueberry mixture until the top is covered. Bake until the apples are tender and the topping is golden, about 30 minutes. Serve warm.