I attended aircraft accident investigation course a few years ago in Texas. The guy who taught it (Mike Grost) was very experience, having investigated hundreds of accidents.
He taught us to recognize debris fields, trajectories of impact, etc. When I first heard about this "Where is the plane if the Pentagon was really hit by one?" junk---I thought it was a prank, a bad joke, a game.
An aircraft traveling that fast and deliberately hitting a building the size of the Pentagon does not leave much in the way of wreakage intact. Look how much of the Pentagon it did destroy--and that building is made of reinforced concrete and limestone.
Tinfoil aside, even this one would be laughable if it were not so tragic.
This was actually debated by the tinfoil hatters on FR. The answer was, of course, "in smithereens."
But, see, you're bringing in facts and logic. How can one possibly have a decent conspiracy theory if you insist on doing such things?