Evidently the system that the military has in such cases failed on the 9 11 and no one can guarantee that it will not fail again, given the same circumstances. The scenario was as straight forward as they get: comm contact with four jets was lost.
The decision matrix is not "comm contact lost, shoot jet."
You realize that, right?
For example, there was no cueing that a particular comms contact lost was out of the ordinary until the first jet hit a building. At that point, during a time in which the presumption of that tactic was not on the table, the timeline to get whatever alerts (and perhaps tankers?) were at hand up, and then within the vicinity of an unknown number of jets of interst (which of the hundreds in the air, and where are they?) across an entire continent does not lead to your posited FOUR opportunities.
Maybe 1, maybe 2, depending on how you reconstruct the time and space problems. As I suspect you are aware, while it is all going down, figuring out which flights are potential hazards takes time.