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.
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.
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.
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.
During his conversation with Rachel in the car outside Falcone's, Bruce's seatbelt is visibly fastened, but he later gets out of the car without unbuckling the belt.
Searchlights like the one Falcone is tied to are incredibly hot. Anyone held against one like that would be horribly burned.
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.
A newspaper article has the phrase "loose faith" when "lose faith" is meant. In the same article, the all-caps "METHAMPHETAMINE" is spelled "METAMPHETAMINE."
A couple times, Rachel is referred to as a district attorney. Since there would only be one district attorney, technically, she would be an assistant district attorney.
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.
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.
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.
Ducard should be unconscious while sliding down the mountain side, but he still keeps his head elevated away from the ice.
The rounds in the revolver have primers which have been colored blue to indicate to all cast and crew that they have been rendered inert.
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.
The speedometer in the Rolls Royce is reading "0" even though the car is supposedly in motion.
In the short scene where Rachel Dawes is driving to Arkham Asylum, the street clearly has three lanes separated by white dashed lines indicating a single direction of traffic, yet traffic is flowing in both directions.
The Gotham City police cars have a large "GPD" on the side but the abbreviation used on jackets is "GCPD".
At Bruce Wayne's birthday party, the birthday song does not match the lips of the party-goers.
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 about 1:34:05: 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.
There is a stunt ramp visible when the second police car flips during the city chase.
During the pursuit of the 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.