The secret part gets me though? Why did it need to be a secret?
Because both of the AF1 planes are awesomely important security assets, and giving terrorists a big heads up about where either one of them is going to be in the air at a given time creates too big of risk of one of them being taken out, leaving POTUS with no back-up plane in the event of mechanical or other problems with the first one.
But, plenty of information could have been disseminated to prevent panic, without specifying that one of the planes involved would be an AF1 plane. I suspect this may be where the screw-up occurred -- i.e. somebody high up in DoD put out the word that the involvement of AF1 must be kept an absolute secret, and somebody between that person and the few public officials who got any information at all, misunderstood this directive to mean that entire mission had to be kept an absolute secret.