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.
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.