And as such, I would imagine that a single Air Force One plane at any given time (either One or Two) would be available for any type of emergency dispatch, as such this would be the only plane the President would need to be aware of or concerned about.
Air Force One (Two) could very well be in the shop for brakes, getting it's upholstery redone, or being retrofitted with a new 52" Plasma. This day it happened to be flying over NYC for a photo op.
Bottom line, someone didn't do their job (on a staff level), and the message didn't get across. Did it scare people? Sure. Should it be news for the next two weeks about how some coffee-pushing moron couldn't deliver a memo and this was the result?
Fire the idiot and move on.