Other mistake: While a sniper is awaiting permission to shoot, a rat crawls up his leg and bites him, resulting in an accidental discharge. A trained shooter, much less SWAT sniper, knows that you never place your finger on the trigger until you are prepared to shoot. Otherwise, you could have an accidental discharge.
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.
Revealing mistake: After Garber shoots Ryder, he is told by the approaching policemen to "drop your weapon". At which point the camera pans to a shot behind Garber where he is holding the gun in his right hand and proceeds to drop it. Watch the bottom of the screen and you will see Garber catch the falling gun with his left hand.
Continuity mistake: Towards the end of the movie when the single train car is rushing down the Coney Island bound F line, you see different camera shots of the train above ground. One of the shots shows the train speeding past Shea Stadium, which is actually located in Queens on the 7 line.
Continuity mistake: When Ryder first walks into view over the Internet feed from the laptop, he is wearing a greyish T-shirt (most likely short-sleeved as well). In the next shot, still on the feed, he's wearing a black leather jacket, the same one we see him wear since the beginning.
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.