I make this Vanilla cake recipe all the time to make regular full size cakes but for some reason when i try to make cupcakes with it the center of the cupcake falls creating a bowl shape in the middle.... why does it do that?

The problem might be under-baking (even if a toothpick comes out clean). Bake a couple minutes longer. Do you want a domed top? Start your cupcakes 50 degrees higher and drop the temp after 5 minutes.