Just after Peter Parker becomes spider-man and it shows fast interviews (someone mentions bug man) well look at one of the guys newspaper - it says bank robbery foiled, he hung the bad guys chopper between the WTC towers. A few seconds later we can see the WTC tower's reflection in the eyes of Spider-man, why? because the bank robbery were a deleted scene, the scene were deleted because of the attack...that's why we don't see the robbery but still see the WTC.