Mix flour, brown sugar, oats, graham cracker crumbs, and cinnamon together in a bowl; stir in butter until well mixed. Press 1/2 the oat mixture into the prepared casserole dish. Spread apples and blueberries over oat mixture; drizzle with lemon juice.
Stir white sugar and cornstarch together in a microwave-safe bowl; mix in water and vanilla extract until smooth. Heat sugar mixture in the microwave, stirring every 45 seconds, until sauce is thick and nearly clear, 2 to 4 minutes. Pour sauce over fruit layer and sprinkle remaining oat mixture over top.
Heat in microwave at 70 percent power until fruit is tender and juice is bubbling, 8 to 10 minutes. Cool slightly before serving.
