(at around 27 mins) After Rachel slaps Bruce in the car outside Falcone's, his hair is messed up; the next shot it's nicely combed; and the next it's messed up again.
(at around 5 mins) When Bruce is thrown off the truck after being released from prison, his bag is several feet away from him. In the next shot it is at his feet.
One Arkham inmate is named Victor Zsasz in the script and source material, but is listed as "Zsaz" in the credits.
(at around 1h 45 mins) When Bruce is hit by the burning wood, it rolls off him to his feet as he falls back and hits the floor. As soon as he hits the floor and is unconscious, its placed as if it landed on his chest.
From 1:01:36 -the barrel of the sub-machine gun goes back and forth from smoking to not smoking.
(at around 1h 5 mins) Searchlights like the one Falcone is tied to are incredibly hot. Anyone held against one like that would be horribly burned.
(at around 1h 26 mins) You cannot open a water main and see water flowing through it. Water mains that feed uses including sprinklers are pressurized to over 150 psi. Opening a main in the fashion shown would have flooded the basement in minutes. Also, mains serving other areas do not pass though buildings.
In the beginning of the movie when the young Bruce Wayne is in the police station following his parent's murder, he is consoled by a uniformed Jim Gordon. On Gordon's shoulder epaulettes there are clearly lieutenant's bars, yet later in the film it is said more than once that Gordon was a sergeant at the time. That rank would have put chevrons on his sleeves and collar tabs, not bars on his shoulders.
Beginning at 1:59:50 until 2:00:57, Batman flies through The Narrows hanging from the elevated train by his monofilament. This is impossible because the monofilament would hit the structure that holds up the train.
In the ending credits "supervising" is spelled "supervsing" missing an "i".
The movie appears to be set in 2005, yet scenes set in Bruce Wayne's childhood feature the same 2000s-vintage automobiles as in the present day scenes. Shouldn't his childhood be in the 1980s-90s? It is common in Batman comic books to fill scenes of Wayne's childhood with deliberate anachronisms, to obfuscate the era when his origin took place.
(at around 1h 8 mins) If the microwave emitter really evaporates all water in the vicinity, in theory it should also kill everyone standing near it, as human bodies consist mostly of water. However, it is mentioned earlier in the film that the emitter uses "focused microwaves" specifically designed to target an enemy's water supply. For the safety of those operating it, the device was presumably designed only to affect water at certain levels of pressure.
(at around 1 min) The position of tree branches over the water well young Bruce falls in changes. The branches look one way (from the bottom looking up) when Rachel calls down, but it appears to be a different tree when Thomas Wayne lowers himself to rescue Bruce. This may be a deliberate, as the scene is a subjective view of a confusing, traumatic moment, when memory can become unreliable.
(at around 1h 30 mins) During the roof jump part of the Batmobile chase there is a police officer who orders Batman not to move on the bullhorn. He is the same actor that later delivers the line 'Can you at least tell me what it looks like?' as the Batmobile whizzes past him. (In mitigation, they could be twins.)
(at around 40 mins) Ducard should be unconscious while sliding down the mountain side, but he still keeps his head elevated away from the ice.
At 0:22:58 -the rounds in the revolver have primers which have been colored blue to indicate to all on- and off-set persons that they have been rendered inert.
(at around 38 mins) During the 'criminal execution' scene, it is clear that the sword Wayne is holding has no edge. It has been squared off for safety on-set.
At 0:19:18 -a plastic water jug is seen on the ice, bottom left.
(at around 1h 40 mins) Bruce Wayne's birthday party - the birthday song does not match the lips of the party-goers.
(at around 1h 40 mins) Before Bruce makes his speech at the birthday party, he knocks at a wine glass twice, producing two differently pitched tones. In reality, it should be the same tone, because the pitch is defined by the level of liquid inside the glass.
As Ra's Al Ghul is placing the blue rose under Bruce's lapel, he says "Tell me, Mr. Wayne, what do you you fear?" The word "you" is repeated (presumably having been resynchronized).
(at around 1h 30 mins) During the wide shot depicting the batmobile sitting idle atop the parking garage, a swift sweep of the SWAT helicopter's spotlight reveals dozens of cast and crew packed into the elevator waiting area.
(at around 1h 35 mins) There is a stunt ramp visible when the second police car flips during the city chase.
(at around 1h 35 mins) During chase of Batmobile after rescuing Rachel from Arkham, the police helicopter pilot says, "in pursuit of vehicle heading west on I-17." Odd numbered Interstate highways run north-south, while even numbered interstates run east-west.
Rachael has been poisoned with a hallucinogenic drug that will "damage her mind" yet she is kidnapped by the mysterious Batman and subjected to, arguably, the most harrowing car ride ever endured by a human being yet she suffers no ill consequences from the experience.
Microwaves cannot penetrate metal, or even a metal mesh. That is why you don't place metal objects into a microwave oven and also why the front of the oven can have a glass window- because of the metal mesh embedded in it. So the whole plot of vaporizing the drugs in the city water lines is a non starter.
The explanation of how the gas works is inconsistent. Wayne's GF has to be rushed to get the antidote or it will ruin her for life. But later people are inhaling it like the little boy she helps for a long time. It's a literal fog over the whole place. Also Rahs Al Guhl and his henchmen use gas masks, but earlier they say that the antidote protects one from the effects of it. They would have inoculated themselves and no need for masks.
Woodworks that are over 100 years old in a damp cave are still in good condition.
Apparently the RICO Act, which was passed in 1970, does not cover Gotham.
The Gotham City police cars have a large "GPD" on the side but the abbreviation used on jackets is "GCPD".
(at around 44 mins) A newspaper article has the phrase "loose faith" when "lose faith" is meant. In the same article, the all-caps "METHAMPHETAMINE" is spelled "METAMPHETAMINE."
From 0:10:28 -a billionaire wearing poorly fitted trousers.