When Batman strings up Two-Face his hands are free. When he is completely strung up, his hands and feet are tied behind his back.
The number of members in the squad of doctors & M.P.T (Medical Protection Team) varies throughout the game.
While inside the Iceberg lounge, there is a large glass dome for the roof. But when outside of the building, there is no dome, only a flat roof.
When Batman activates the secret panel to enter the Chamber of the Demon, he deduces that a sword is required to open the door. But in the assembled footage previously shown, the assassin does not use her sword at all.
This version of Penguin has the bottom of a broken bottle jammed over and around one eye instead of a monocle. It is explained it has not been removed because that would risk severing major blood vessels and killing him. However, there are no such blood vessels near the eye, and since the bottle remains a protruding object with sharp edges, any mild impact could move it enough to cut those as well.
There is absolutely no way for any Mayor to give a private security force enough power to just randomly arrest people who politically oppose them (among them well-known figures like Bruce Wayne and people working at the press like Jack Ryder) and throw them into jail without any trial.
The TYGER helicopters lack tail rotors. Without either a tail rotor or a counter-rotating rotor, a helicopter will spin uncontrollably in the opposite direction to the spin of the main rotor.
The Deadshot side mission ignores all the laws of physics to justify the assassin's ridiculous kill shots.
When Batman is hunting Deadshot, his second victim is sniped through a full water tower. Even assuming there was a gun that could still be lethal after shooting through 6 feet of water (and MythBusters confirmed there is not), the bullet's trajectory is completely unaffected.
All of Deadshot's bullet trajectories follow straight lines instead of parabolic arcs like they do in real life.
Deadshot's bullet trajectories are determined using only a single point of impact, which is impossible. Indeed, the trajectory of Joker's bullet can only be traced using the bullet hole on the floor and the hole in the window.
One of Deadshot's victims is killed by a bullet ricochet, something the MythBusters also proved to be impossible.
Fire extinguishers can be used by NPCs by being thrown and then rupturing and causing damage. Fire extinguishers are designed to be difficult to rupture.
After infecting Batman with his poisonous blood, Joker says he had also shipped some all over Gotham, possibly infecting even more people. By the game's end, Batman manages to cure himself, but it is never mentioned if the other people in Gotham managed to be cured as well.
It is implied, however that the cure likely will be sent out to the other infected by way of mass producing the cure which is now within Batman's bloodstream.
Spelling and grammar mistakes in subtitles.
If an enemy NPC hears a repeated line from the Joker or another super villain monitoring their heartbeat monitors informing them that one of their number is unconscious, they will say to do what is said, even if the Joker or other super villains aren't asking anything.
When the mechanical guardians are being interfaced with, they break down at the end of their interface. Since they are only being interfaced with, they should not suddenly break.
The mechanical guardians still show signs of power despite being out-of-use for decades.
The Batman can somehow rip grates out of the wall. The bolts that are used probably can hold hundreds of pounds, so it is more likely that he would have some sort of tool to deal with them.
There is no reason that the steel mill would be active since the only people occupying Arkham City on a regular basis are criminals.
The setting is in the United States of America, yet the measurements are in metric.
Batman identifies Riddler's informants using facial recognition, though many of the Riddler's men wear full-face masks.
In the Arkham series it has been repeatedly said by Batman that he will not kill yet you clearly see that Batman pushes a blade through Ra's as they fall after Wonder Tower explodes.
The Batman and his allies sometimes use names, which is never a smart thing to do over a radio channel.