 FACT: When the ship floats over New York, it goes over the Empire  State building, and the needle of the building is within yards from  the ship. At that time, the World Trade Center was, in reality, much  higher up, yet somehow the taller buildings are not damaged from  colliding with the ship. Also to note in a later scene when they  show the invasion ending at dawn, one of the towers is still  standing and intact.