Air Force One's livery is white and blue, not white and red.
At the altitude Air Force One would be flying, Spidey would have suffocated and/or frozen to death outside.
When Doom's blimp overtakes Airforce One, seen from above, the edge of Airforce One's wing moves over the blimp instead of beneath it (animation cel layering mistake).
When Betty says hi to Peter, her face is a completely different shade of pink than her neck and hands.