At about 39:30 in the episode, there is a transition showing a Philadelphia, PA police SUV driving past the front of a police station. There are several Philly police cars. About four minutes later, the police cars that arrive at the school are "Metropolitan Police" or Washington, DC police and DC license plates.
In the first episode of season one, Lightman's Mother was very plainly English, in season 3, episode 9, she is broad Irish.
Eli Loker calls Lightman to tell him that Jacqueline Mathis is in custody at the "2nd District". They go to the Philadelphia Police Department's 19th District in the next scene.
When Lightman is speaking to James for the first time in the prison, after asking him how he felt about his teacher dying, the boy responds, "I prayed for her soul." Jehovah's Witnesses do not believe in the existence of a soul.
A photo of Kay Panabaker can be seen on Lightman's desk. That's because in the original pilot, she played his daughter Emily. Her scenes were removed and the role recast, but the photo remained.
When Dr. Lightman (Tim Roth) visits the jail to interview the teenage suspect, he looks down through a barred window that has had a bar cut out so the actor's entire face is visible.