Zeev's Turnips Talk Politics (ZTTP)

[Math Junkie]

Another possibility to consider is that what Bush may have seen was the second plane crash. This occurred at 9:03, just a few minutes after he arrived at the school. Here's a video of that second crash:

http://news.bbc.co.uk/olmedia/1535000/video/_1537652_wtc13_evans_vi.ram

Note the actual wording of the quote from your link:

"I was sitting outside the classroom waiting to go in, and I saw an airplane hit the tower..."

Notice that in that video, it appear as though the plane is hitting the first tower, whereas it is actually hitting the second one which is hidden behind it. As he says, he was whisked off and didn't have much time to think about it, so it's possible that it may not have registered in his mind that the building was already on fire when the plane he saw appeared to hit it.