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 a 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 looks like coarse crumbs.
Add the milk and vanilla. Stir just until a moist dough forms.
Turn the dough onto a work surface coated with flour. With floured hands, knead gently 6 to 8 times until the dough is smooth and you can work with it.
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.