This first level of analysis was on my former web site (see archive), put on line in september 2002, with some differences in the numerical values, but the same conclusion.
If we don't focus on the assumed presence of a flying object having caused this explosion but only on the explosion itself, frames 1 and 2 can't be in succession in the film, separated by 100 ms. Assuming that the blast propagation in the air occurs at a rather regular speed, close from the sound speed in the air (300 m/s), we should see at least one frame showing the beginning of the explosion, perhaps more !
Assuming that there are no lost frames, and that a 757 has moved from frame 1 (hidden by yellow cabinet) to frame 2 (masked by explosion) beetween frame 1 and 2, in 66 to 100 ms, we must admit that this plane has covered a distance equal to :
If we assume that the 757 was about full speed, 900 km/h, or 250 m/s, the necessary time to fly over 85 m is 340 ms. This means that three frames have been lost. There is, obviously, a total lack of chance to loose the three frames of this video on which the 757 could be seen, crossing majestuously the space beetween the yellow cabinet and the pentagon, and crashing itself on the wall of the pentagon !
Thierry Meyssan first emited the "missing 757" theory in his book "L'effroyable imposture", followed by Pentagate. The violent attacks against the person of Thierry Meyssan, more than against his theory, have reinforced this theory to the eyes of those who interpreted this as a lack of arguments.
From an engineer's point of view, at this first level of analysis, it seems obvious that it could not be a 757 seing the web site of : XOX , who made a fantastic 3D reconstitution : see for example image below. The glasses and cross-bars in some windows are not even broken at the exact place where the plane wings should have hit the building !
A pilot who saw the impact, Tim Timmerman, said : "The nose hit, and the wings came forward and it went up in a fireball." Coming forward, which is normal from a structural point of view in case of a shock on the nose, the wings should have hit the building and broken on their whole span the glasses and the window crossbars at least !

See aerial photo on "defenselink" web site :
See also photos of pentagon's front before collapse. The yellow cross is the assumed impact point
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Given the wingspan of a 757 (38 m), it's cabin's size and it's tail height, either there should be much more damage on the front, or - assuming it was hardly reinforced - more parts of the plane should have rebounded and be found on the lawn outside. See below one of the pictures taken after the crash.

Taking as references images of crashes against buildings, (the El Al 747 in Amsterdam - crash description, photos -, Concorde of Air France at Roissy), it is difficult to imagine that the scene of the Pentagon and surroundings after the crash (the lawn intact, ...) is the scene of a 757 crash.
The approach of a 757 towards this building leave a lot of questions unanswered : realism of the approach trajectory, position of the impact point, no track of the engines or landing gear on the grass, no damage made by the tail on the building...
Two explanations - not exclusive - can be found to these paradoxes :
This would explain why these frames have been "lost" : they are those on which one can recognize that it this not a Boeing 757 which hit the pentagon and/or which show how this plane exploded. The first to claim for this thery was the french journalist Thierry Meyssan : according to him, something (a missile, a remotely piloted plane) was directed on the pentagon, in order to increase the gravity of the attack of 9/11, the pentagon being a military target. The various materials available, including the cctv images released by the DOD must be analysed carefully, in order to try to confirm or infirm this hypothese.