Riddler seems to be able to still broadcast his messages even if you've taken him into GCPD custody. Sometimes he will appear on the screens taunting you or if you attempt to use one of his Riddler Rooms afterwards he says you can't do it again.
The Batman only synthesizes one antidote injection for Dr. Langstrom, but he is seen injecting him twice.
Considering that Scarecrow no longer has any actual lips, he shouldn't be able to actually pronounce about half of the consonants of the alphabet. "B" and "p" sounds are the most egregious.
During the side mission 'In the Line of Duty', 16 firemen need to be rescued. All sixteen apparently came from one fire truck, yet no fire truck holds that many men.
The Order of Saint Dumas claims they have watched over Gotham for more than five hundred years. Which is quite a feat, considering the first permanent European settlements in America were established in the mid-16th century.
Pressure vessels such as fire extinguishers are shown to rupture. Pressure vessels are specifically designed to not rupture violently.
On the final test for Azreal on top of the Lady of Gotham he waits by a burning bat symbol as he was for the other trials. But if you look at the bottom of the platform he's on the burning bat symbol is on the side of Bleake island. If you look at the bottom, you can see it's on the side of Miagani island.
Spelling and grammar mistakes in the subtitles.
During a special mission where the Batman investigates the death of several missing people, the Batman states that one of the dead is missing several toes, but his toes are completely intact.
One of the Batman's moves is to plunge an enemy by the head into an electrical box, disabling him. Doing this is more likely to kill a man rather than disable him, and killing is something the Batman scrupulously avoids.
One of Two-Face's eyelids was burned off in the event which made him. An eye without an eyelid would become dried out and go blind.
Dr. Langstrom is mutated into a bat-like creature during an experiment. The Batman synthesizes an injection of DNA to reverse the mutation. It should take months of gene therapy to be able to do this, not just a simple injection.
There is a safe inside the water filtration plant. A safe this size should not be in a water filtration plant.
In the Batgirl: A Matter of Family DLC, which is set between the events of Arkham Origins and Arkham Asylum, the mantle of Robin is held by Tim Drake in his suit from Arkham Knight. At this point in time, the mantle of Robin should be held by Dick Grayson or Jason Todd.
Although taking place in the United States of America, all the measurements are in metric.
At one point Batman risks his own safety by jumping into the toxic gas cloud to fix the Batmobile, telling Alfred there is "no other way." However, numerous times in the game the Batwing is able to pick up and carry the Batmobile, and later in the game it's revealed that Lucius Fox has a second, identical Batmobile on-hand and ready to go.
The Batman and his friends use first names on occasion - not a wise idea in case someone hacks their communications.
After defeating Harley Quinn's minions in the movie set quarantine section, the Batman and Robin simply leave them there, telling Mr. Adams to not let anyone in - pointless, since there are so many of the minions unconscious but alive within.
When Batman rescues the fire chief, he refers to him as "captain".
Scarecrow looks and sounds nothing like he did in Batman: Arkham Asylum.
The Batman refers to a dead man as 'they'.