When the president (Harrison Ford) uses the escape pod to get away from the plane, you can see from the outside that the escape pod comes out of the back of the plane. But, later on when the people are escaping with parachutes, they are jumping out of the back, where the escape pod was.
My theory is that they have a hatch on AF1 to cover up the hole where the escape pod was/is, to keep the amount of drag down on the plane, which slows it down.
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