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.
When Dective Kenny Solomon checks on Ameila 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.
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.
When the detective's car is about to enter the abandoned slaughter house compound, and as seen from the front, the lights are turned off. You then see the car, from the rear, pull up just inside the compound with the rear lights on. The detectives get out of the car and turn the lights off.
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.
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.
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.
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.
The goof items below may give away important plot points.
In the scene where Richard is testing Lincoln's heart monitor with a Fluke, he is only using one lead, instead of two. This may be a deliberate flourish related to the twist regarding Richard's nature.
In the scene where it reveals Amelia killing Richard, she is seen shooting him in the back. However, when you see her shooting him several times, there are no signs of blood or gun shot wounds where he should have been shot.
Just before the reveal of the killer, a very serious and peeved Captain Cheney walks toward Rhyme's apartment, swinging his bare hands in stride. In the very next scene, he is shown dead in the hallway wearing black gloves just like the killer's. This is likely a plan by the killer to frame Captain Cheney for the crimes.