Factual error: When Pelham 123 gets split in two (as in it's uncoupled from the rest of its train), they do so from a control panel from the inside of the car above the seats. Subway cars, like all rail cars, can only be split manually through a lever near the coupler, not through a control panel. In addition, subway cars have ropes between cars, which must be taken down before cars are split. Otherwise they will still stay connected.
Factual error: The 6 subway runs from Pelham Bay Park in the Bronx to the Brooklyn Bridge stop in lower Manhattan. How the subway switches to the F line to Coney Island which is not connected to the 6 line is not explained. It is not possible as the tracks do not cross.
Factual error: When the bad guys go though the hidden exit, they're identified at being around 33rd street. They take an elevator up to the Waldorf Astoria kitchen. This is impossible as the Waldorf is on 50th Street.
Factual error: In the street shootout scene, the two bad guys are surrounded by police officers, the police engage them, which created a crossfire situation. Police officers are trained to be aware of what's down range or what's behind the target they are engaging. The shootout wouldn't have occurred in this manner as they were trapped - the officer with the clearest shot would have engaged them. (01:32:00)
Answer: The hijackers did notice it. There's a scene where they notice it: look at the girl on the screen and then laugh. They get kicks from toying with people, which is why they didn't smash the laptop and just let the guy keep using it.
You're probably right.