Preheat the oven to 400 degrees F (200 degrees C).

Toss apples and blueberries together in pie crust.

Combine 1/4 cup flour, white sugar, cinnamon, nutmeg, and salt in a bowl. Stir in yogurt, egg, and vanilla extract; pour over apples and blueberries.

Combine remaining 1/2 cup flour, pecans, oats, and brown sugar in a bowl; cut in butter with 2 knives or a pastry blender until mixture resembles coarse crumbs. Set aside.

Bake in the preheated oven for 15 minutes; reduce heat to 350 degrees F (175 degrees C) and continue baking until crust is lightly browned, about 30 minutes. Sprinkle crumb mixture over pie; continue baking until golden brown, about 15 minutes more. Cool before serving, about 20 minutes.