Other mistake: On-board Flight 93, Mark Bingham's conversation with Tom Burnett about sports is repeated twice in two separate scenes. You can tell if you listen out for Bingham's line, "You take out all your aggression and all your, you know, all your shit for the day." The dialogue is heard in the background the first time around and then given more focus the second time. (00:46:49 - 00:55:35)
Other mistake: At New York ATC, the radar shows American Airlines Flight 11 disappearing over Manhattan, indicating that it has just crashed into the North Tower. This occurred at 8:46 a.m. Around a minute and a half later, Sgt. Jeremy Powell at NEADS directs the scrambling of fighter jets in search of American 11. He states that the time is "0846" (meaning 8:46) - should be 0847. (00:34:55 - 00:36:17)
Answer: The hole where the plane went into the building is shaped very specifically where you can see the outline of the wings, the middle of the plane, not to mention its size. The holes on the other side of the building did not have this same outline. It wouldn't be difficult to determine that was the point of entry. Not to mention the CNN report focused very heavily on the point of entry hole on the north tower and hardly focused on the other sides because of it until the 2nd tower got hit. They were very clear in the report where the hole was where it got hit. Wasn't difficult to determine with both witness reports coming in fast and the shape of the outline.