The official accounts of radar/transponder tracking and communications problems with following Flight 77 tried to explain how the weaponized airliner was allowed to get within a few minutes of its target undetected. In total this has been taken by many (including myself) as an impossible or at least suspicious string of errors, allowing a third successful attack one hour into the new war. The Pentagon WAS protected by a mobile air-to-air missile defnse system, or was supposed to be, and the system failed as fighters were first alerted of the danger by a columnar smoke signal saying mission failed.
A useful new entry at 911 Myths regarding this - Losing Flight 77 - is up now to shed some light on it. I haven't really read it yet, this is just a tip-off. Calling on arguments by the relatively respectable and non-loony 9/11 Scholar Nafeez Ahmed, the 9/11 Commission Report and hearings, original interview with Colin Scoggins, and more, Mike W concludes:
Not a single one of Ahmed's arguments entirely withstands scrutiny, then. His most substantial point comes in the differing NORAD timeline, but the problems here are well-known, and Ahmed fails to provide independent confirmation to show that their version of events was correct. What's more, the NORAD tapes (released in full after Ahmed completed his book) contradict their timeline, for example clearly showing that they knew nothing of Flight 77 until after 9:30 on 9/11. And so while Ahmed claims victory, the reality is very different: the balance of evidence continues to support the 9/11 Commission timeline for Flight 77.
Additional discussion at JREF with technical input from Gumboot.