At the end of the game, in the news broadcast, it mentions Scott Shelby's age as 48 years old. However, when we are shown his headstone, it gives his birth and death dates as 1967-2011 which would make him 44 years old at the time of his death and not 48.
When Jayden makes his first recording with ARI on the wasteland where Jeremy Bowles' body is discovered, he notes that date as October 2011. Later, when Madison checks into the seedy motel, the clock behind the receptionist displays the year as 2012. Pre-release media such as the game trailer do show this clock displaying the correct 2011 year.
Towards the end of the scene at Manfred's store when Manfred is discovered dead, Lauren quickly finds and takes his list of Royal 5 typewriter repair clients and talks to Scott about it in their next scene as if she's the one who took it. Yet in the later scene where Scott is revealed to be the Origami Killer who has been collecting the evidence on himself to destroy, he has a flashback to the Manfred scene that shows he took the list himself.
When Madison checks into a motel she puts her date of birth down as May 3rd 1984 which would make her 27 years old at the time of the game setting. If she dies in the game however, her gravestone says she was born in 1981 making her 30 years old.
Scott Shelby asks to buy an asthma inhaler from the convenience store. Asthma inhalers are a prescription medication and wouldn't be available from a convenience store. He would have had to take a prescription from his doctor to a pharmacy if he needed a new inhaler.
Ethan, while aided by Madison, can evade arrest by taking the subway. Police officers can contact transit authority to get the subway train stopped at the next station precisely so that fugitives cannot escape this way.
If Ethan is arrested and interrogated by Blake, Norman has the option of interfering by shoving Blake and then punching him. Blake will then force Norman out of the room by threatening him with his gun. It is against police protocol to carry a sidearm into interrogation, for fear the suspect might get possession of it. This rule is deliberately violated by Blake to demonstrate further corruption. Other examples of disobedience committed by Blake include trespassing on a suspect's property and using excessive violence towards them. This is used to make the player consider Blake a possible suspect in the case.
The game is supposed to be set in the United States, yet Ann Sheppard's hospital room has "Type-G" wall-sockets next to her bed. These sockets are meant for 220-240V/50Hz European voltage, and would never be found in an American hospital.
The game is supposed to be set in the United States, but some of the cars that are featured have European-style license plates. The most obvious example is the sports-car Ethan picks up in "Chapter 18 - The Bear".
In the beginning of the game, Ethan receives a poison pen letter from the killer which is very clearly threatening him and his child, reads it, reacts to it, but then does nothing about it.
In the Welcome Norman chapter the time at the start of the chapter is given as 7:55 PM, yet sunlight is seen through the window of his office and Leighton Perry tells his secretary to "cancel all appointments this afternoon." when it's in fact evening, both of these put together indicate that the chapter was potentially supposed to take place earlier in the day but was changed to later without any other changes to reflect that.
If Ethan kills the drug dealer, he vomits on the floor afterwards leaving his DNA. Yet the police never tie this back to Ethan and it's still possible to get an ending where he lives happily and free.
Madison can be seen by police trying to help Ethan evade arrest. Yet she is never pursued or arrested for aiding a fugitive.
The Origami Killer's stature is quite large, he would have a large amount of difficulty spreading the glass out in the tunnel for the Butterfly trial, Ethan who is smaller and thinner barely fit.
Ethan takes the box he receives from the Origami Killer to the motel and after each trial returns to the motel to retrieve the next figure for the following trial. If he had simply kept the box or even just the contents with him he could have gone straight from one trial to the next and got to his son much quicker and yet he doesn't do this and instead prolongs the time before he gets to Shaun, risking Shawn dying before Ethan got to him.
If Ethan avoids arrest the first time but is then arrested the second time and Norman Jayden is still alive, Jayden doesn't point out that he fought the real killer at the night club and his body type was clearly different to Ethan's.
The player can listen to the thoughts of the playable characters at various points in the game. Yet the thoughts of Scott Shelby at various points appear to contradict the later reveal that he is in fact the Origami Killer.
When Madison is tending to Ethan after he has attempted The Butterfly trial, if he has burns she attempts to bandage them, which could easily cause the burned skin to attach itself to the bandages and peel off painfully. She also only treats the cuts on one of his arms and completely ignores the cuts on his legs.
The psychologist that Ethan sees tells Jayden and Blake that he cannot tell them anything that he and Ethan have discussed, whilst this is generally correct he can tell them if he suspects Ethan has or will harm himself or others.
Multiple characters pronounce the word "origami" differently to each other and differently to the general American pronunciation.