There is a group of expert aviation professionals who have had a website up for several years.During their careers some of them even flew the aircraft that were purportedly destroyed on 9/11.
A couple of years ago they got the Flight 77 black box data from the NTSB, who had received those black boxes from the FBI, because the Pentagon was a crime scene.
When these aviation experts put the flight data recorder ("black box") data into professional flight simulators (the type used to train professional airline pilots) it did not add up.
For one thing, the data showed Flight 77 at about 400 feet high at the time of impact with the Pentagon (not possible in this universe).
The NTSB would make no comment when the pilots inquired about the discrepancy in the data NTSB said was the official data.
Further perusal of the data indicated that the flight deck door (door to pilot cabin) remained closed during the entire flight. In other words, no one from the passenger section opened the door to get into the cockpit.
Thus, these professionals are concerned that the official story is wrong or that they and/or the NTSB were given the wrong data.
UPDATE: The comments to this post show that some folks do not comprehend the very critical importance of Flight Data Recorders in terms of determining what caused an airliner to crash, what happened on the flight, as well as what did not happen.
Clearly, the best science is used to make sure that these "black boxes" work accurately:
Both the Flight Data Recorder and the Cockpit Voice Recorder have proven to be valuable tools in the accident investigation process. They can provide information that may be difficult or impossible to obtain by other means. When used in conjunction with other information gained in the investigation, the recorders are playing an ever increasing role in determining the Probable Cause of an aircraft accident.(National Transportation Safety Board). Our ability to believe as well as our inability to believe certain things is a psychological reality which some people have no control over, exclaiming "I could not believe it even if it was true".
If you find yourself saying "I don't believe the Flight Data Recorders" because you have already determined what happened on a flight, you are at the edge of the realm of your capacities of belief, so be careful not to proceed recklessly until you are ready for it.
Like the man said, if "you can't handle the truth" apples, don't deal with it until you can handle it. This is for your own mental health's sake. We do not want anyone who is not qualified to sit on a jury to deal with adult jury material to their demise in any way, shape, or form.