Many Eye Witnesses said they saw a missile. Even better many military officers first on the scene said they smelled cordite (click to learn about cordite)
. They were heard on the news right away, but never aired again later. You can still find the interviews in google and you tube videos though :D.
As for the WTC many people running out of the building described secondary explosions on various floors. This includes Fire fighters and police officers. These two were aired right away then never aired again.
One thing that is VERY odd is bomb sniffing dogs were halted from going through WTC a week before the attack. They were made to leave the building abruptly. That is fact.