Plot hole: During the scene where Ramus is shutting down the power in the tunnel, he shoots off a padlock with a gun with one shot. Aside from being quite dangerous at close range, both Mythbusters and Masterlock have proven this cannot be done with an ordinary gun and ammo, and certainly would be unlikely with one try. I know this used to be run-of-the-mill stuff in movies, but it does not fit modern research that has been done concerning the strength of padlocks vs using guns to open them.
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.
Continuity mistake: The Brietling John Travolta is wearing is different from scene to scene when he is on board the train. One watch has 3 dials; the other none.
Other mistake: In the scene where Garber is in the helicopter, the far away shot shows it as being almost sunset, when it is actually closer to 3:30. The sun is low on the horizon.
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.
Other mistake: Following the scene where Phil Ramos is shot in the head by the sniper, you will notice him still breathing behind Ryder showing him in the background when Ryder gets on the radio.
Revealing mistake: The police car that transports the money is not what is used in actual police work. The all dark blue and white accents you see in the film is a color-scheme used in traffic cars and school safety cars. The real police cars are white with dark blue accents.
Visible crew/equipment: When Garber drops the gun after shooting Ryder a hand quickly comes into frame to catch it.
Plot hole: If Travolta knows there is going to be a market-altering event, he can structure investments to take advantage of that without having to physically be on the train. Why didn't he let the other guys be idiots and hijack that train without him? He'd still get his ~$300M profit, with much lower risk. Any real Wall Street guy would understand how to maximize return while minimizing risk.
Audio problem: When Ryder clicks the Google link about Garber, the page makes beeping sounds when the news article flows down the screen. That never happens. Pages just appear silently.
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.