When bullet is passing through the apple, the apple skin is in the same direction as the bullet when the bullet comes out, why is this?

How scientific do you want your answer to be? The bullet is pushing whatever is in it's path out of the way, including air, the apple itself, and the apple skin. The skin, being attached to the rest of the skin which is attached all around the apple, breaks forward and outward only enough to let the bullet go by. The speed of the bullet is decreasing through air and then again through the apple and apple skin, and again as it continues on.