I just stumbled upon this info from a few years ago regarding the four flights on 9/11. For me, it makes more sense than anything else I've come across regarding what happened to the flights and passengers. It is a long read, but in my opinion, well worth the time.

Hope you enjoy!
C-lo
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Most people are not aware that there are issues with the 4 groups of people who flew on the 4 flights of 9/11 from 3 locations. There are so many issues it would take a newsroom full of dedicated reporters a long time to sift through it all. There are problems with the boarding of passengers on 3 flights. And on the 4th flight we find 2 boardings, an unusual event to say the least. Two of the aircraft, we are to believe didn't even take off on 9/11, as this is what registers in the BTS database for flights 11 & 77 on 911. Two of the aircraft that allegedly struck the towers, can be plausibly shown to be drones, calling into question both passenger and crew from those respective flights. (11 & 175) While flight 77 obviously didn't crash at the Pentagon from all evidence shown, and flight 77 is one of the 2 flight which BTS shows no departure time for. While flight 93 wasn't even a regular flight on 9/11, it was created in the last 2 hours before it flew. And as you will see are good reasons to believe Flight 93 was boarded twice at Newark. If this sounds confusing, it is because it was meant to be so. But I believe this article shows it is possible to make some simple sense out of the days events and tie them all together.

More here... http://letsrollforums.com/happened-passengers-4-flights-t20496.html