Patterson has Grace, John, and Charlie in his office after the fight on the money train. After dismissing Grace, he locks the door to his office. Patterson's assistant enters the room to inform him of the confession.
Patterson orders police deployed on the station platforms at Grand Street, but they actually appear in the tunnel.
When John and Grace talk after their boxing exercise, Grace's gold crossdisappears and reappears between shots.
When Charlie is going down to steal the money train, we see him going down at the 110th street station, on the B and C lines. Moments later, just before Charlies lies down on the tracks, on a pillar behind him, it says 116th street.
Chasing the arsonist at Fulton Street, John tries to cross the tracks but is trapped momentarily between trains passing in both directions. At the same time Grace and Charlie are running along a nearby part of the platform, but the trains are not there; in fact, our viewpoint is from the opposite trackway below platform level.
In a collision between a train car and columns, the columns would tear the train car apart. This has occurred numerous times in the past decade, most infamously in the Union Square wreck in '91, in which columns installed nearly 90 years earlier tore in half a runaway 6 year old train car.
It is impossible to "bleed the brakes" or otherwise dump out compressed air on any NYC subway car and force a runaway condition. When air pressure is lost on a subway car, it actually engages the brakes. This is a common fail-safe in rapid transit and railroad systems.
Until January 2006, the real money trains (officially known as "Revenue Collection Trains" of which there were several dozen cars in service, not two) were usually older, grungy, decrepit retired passenger cars with bars on the windows. They were painted yellow with black warning stripes in the front. They were staffed by NYC Transit Authority, a majority of which appeared to be middle aged, overweight, and female, oddly enough, and armed with nothing more than .38 revolvers. They were nothing like the automatic weapon-wielding SWAT team cops depicted in the movie.
The ticket booth windows in the New York subways are bullet-proof, so John would not be able to shoot out the window in order to save the clerk. Likewise Grace would not be able to shoot at "Torch" from inside the booth
Glock handguns do not have safeties or hammers.
John was not present while Charlie was getting beat up in the bar, thus making it seem like a goof when he says "Who you callin' nigger?" to Mr. Brown. However, the bartender later showed up at John's apartment to tell him about the trouble that Charlie was in, and it's possible that he told John what Brown said (assuming Charlie told the bartender, which, again, is possible).
NYC subway trains are electric, and get their power from a 'third rail'. This is an extra rail with a safety cover on the outside of the running rails - a 'pickup shoe' extends from each car and rides along the top of the third rail to supply power to the train. This third rail is notably absent in all shots where the rails are visible, because the real NYC transit cars used on the set were converted to run on propane.
When John gets to the escalator in the subway, it's moving, but in the next shot when he is going down, the escalator is not moving
Torch gets into the money booth and squirts the accelerant all around inside the booth and on the clerk (This time, her blouse can be seen to be wet). He throws the match at her and sets the booth on fire, but not her.
A radio message dispatches emergency services to "Fort Hamilton" station, but there are three different Fort Hamilton Parkway stations on different lines (F, N, and B and M), so they would not know where to go.
When Charlie wakes up John by bouncing on his bed and John pulls a gun on him, you hear the sound of a revolver being cocked. The gun appears to be a glock which has a completely different sound when being cocked and generally requires two hands, where only one was used when pulling the gun out.
When John jumps his motorcycle in front of the Money Train, he lands on plywood sheets that are placed between the rails to act as a smooth landing zone for the motorcycle.
Reflected in the rear window just before the collision.
Many instances where a line is shown with the wrong number of tracks, or station platforms are on the wrong side. For example, Wall Street (Lexington Avenue line) has outside platforms, not a center platform; Bowling Green station has no express track that would allow one southbound train to run through while another is at the platform.
The 3 train is an express, but this one is on the local track; yet it runs through the station without stopping, even though expresses stop at Times Square.
Charlie climbs down onto the track and lies in front of the money train, all in plain view of its driver, as if he knows what's going to happen next -- the driver just stops the train right on top of him and says nothing about it to anyone.
Train cab drivers are taught to immediately apply emergency brakes in case of people on track, yet in the fight scene between Charlie Robinson and Terry Edwards the cab driver honks (i.e. does not panic) and the train keeps going (no screeching brakes are heard). The emergency brake override only concerns passenger-operated switches; such an override is active during tunnel sections because in case of a fire firefighters would have troubles reaching the train if it stopped at a difficult to access location.