Goofs

(at around 1h 35 mins) Amelia spends several minutes in the waters of New York Harbor, then heads for the subway station in perfectly dry clothes.

(at around 36 mins) When Rhyme has had everyone set up in his home and they are working on finding the wife, every scene in his apartment shows it to be storming quite heavily outside but when Amelia and the other detectives step outside it is a bright sunny day.

(at around 48 mins) Amelia's case seems to make its own way around the tunnels when she goes to examine the body that was steamed to death.

(at around 4 mins) In the very opening scene, Lincoln, a quadriplegic, wakes alone from a nightmare and the shot from above shows his knees are bent and parted. In the next shot, his legs are perfectly straight with only the feet tenting the sheet.

(at around 57 mins) When Detective Kenny Solomon checks on Amelia at her apartment, he enters through her kitchen window. After he enters the window is shut. Then they go into the next room and you see the window open in the background.

(at around 1h 4 mins) In one scene of the investigation, Donaghy receives an invoice from the FBI stating that the rodent hair follicles were "shaved off". Follicles are embedded in the skin and cannot be removed by shaving. Shaving only removes the hair shaft.

(at around 55 mins) When Rhyme is examining Donaghy's personnel file after she refuses to cut off the victim's hands, he sees a letter from the Commanding Officer dated November 6th 1997 regarding apparent suicide which in the body of the letter prognosticates the suicide two years later of John Donaghy on November 6th, 1999.

It is established early that the date is early November, yet constant thunderstorms take place over several days. November thunderstorms in New York City are an exceedingly rare event.

(at around 1h 13 mins) By shooting and killing a rat, Amelia has contaminated the crime scene that she was sent to investigate.

On the other hand, she was preserving more important evidence that may remain on the body.

(at around 43 mins) The underground gallery was washed up by the high pressurized steam, making impossible to find any fragment of evidence.

Lints and fibers and prints won't survive, but any more solid evidence would.

When the traffic cop pulls over the cabbie/murderer, he leans his head completely into the driver side window. No policeman properly trained would put him/herself into such a vulnerable position.

He wasn't a traffic cop, though. If the Taxi Inspector had proper police training, he would not have done that.

The police, in order to gain access to the victim, had to blast an opening into the underground chamber. This wouldn't have been needed since the killer was able to enter it without using explosives.

The police didn't know where the killer's secret entrance was in the labyrinth of old tunnels and they didn't have time to search.

(at around 27 mins) When Rhyme and the other police are examining the evidence on the track, Rhyme refers to the bolt as "iron" but doesn't find out until later that the bolt is iron, not steel.

He called it iron because he recognized it as iron. There's a visible difference.

In the opening credits, the badge number is shown on Lincoln's hat. However, it is a different number from the badge on his shelf display.

(at around 1h 35 mins) When the girl is rescued from the river, she received paramedical assistance. But the breathing mask is upside-down.

At various points in the film, Donaghy was in underground chambers and sewers. She was in constant radio contact with people on the surface, but radio waves wouldn't have penetrated the concrete and steel reinforcement.

(at around 39 mins) When the murderer is to turn the steam-pipe he just unbolts the valve flange and then push it to turn it. this is impossible to do, besides you can see the pipe elbow is bolted on the pipe that continuing out of the picture.

(at around 38 mins) The view from the car window does not match the swerving you'd expect from Amelia's frantic steering and the screeching sound effects as she drives to the wife of the first victim.

At approx. 19 mins, a very long train is coming through the tunnel, which Amelia stops close to evidence. Yet only one minute later, she is seen taking pictures on the tracks, with no sign of the train.

(at around 1h 35 mins) When Amelia must investigate the Navy Street Station for evidence, she descends into a subway tunnel. However, the old Navy Street Station in New York City was actually an elevated, above-ground station.

Donaghy was a street cop. It makes no sense to have her work a case as a forensic technician, especially a high profile one, if a) she had no desire to work in forensics, and b) she had no training in it.

Donaghy was told to cut off a dead victim's hands in order to remove the antique shackles without damaging them. It would have been easy to make thin minimally-damaging cuts in the hasps rather than cut off the corpse's hands.