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.
Other mistake: When the man is saying the train will stop when it hits a red signal, the child immediately says that they're all green. From where this child is sitting with his mother, and with how short he is, there is no way he could have seen the signal lights. (01:51:00)
Visible crew/equipment: When Garber drops the gun after shooting Ryder a hand quickly comes into frame to catch it.
Other mistake: The young man's computer is discovered and then powers off because it was at 0% battery life. Just after the scene where Garber separates himself from the Ryder and his crew, the man reopens his computer, with it immediately reconnecting to the internet chat with his girlfriend. Obviously, there is no way that the computer would have powered back on without being recharged, let alone reconnecting to the internet and picking up at the exact place where it left off. (01:25:35)
Continuity mistake: When the police on the motorcycles are delivering the money bags, there are 4 of them. When they're walking through the Waldorf Hotel they only have three bags. With watching the hostages they wouldn't have time to consolidate the bags. (01:04:00 - 01:29:00)
Revealing mistake: When the bald guy robber first takes out his gun and begin shooting at the ceiling, it's obvious that he shooting blanks as when they pull back the shot, there is not one bullet hole in the ceiling anywhere along the subway car. (00:12:00)
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.
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.