Ripcord gets hit by a fast-moving car as he falls out of the van in his suit. But when we see the direction from which the car was moving, there is no road, only a hedge.
In there flashback Duke is wearing the gold oak leaves of a Major. When General Hawk first talks to Duke he is addressed as Captain.
The Joes are 2 km from the Eiffel Tower when they report the area is being evacuated. When they finally arrive at the tower, the area beneath the tower is crowded.
When Duke and Ripcord are chasing the Hummer, in several shots the Gatling Gun is shown mounted on their right arms, but when they fire the Gatling gun at the Hummer, Duke fires from his left hand.
When young Snake-Eyes comes into the kitchen it is pouring rain outside. When the quick fight stops, his clothes are completely dry; only his hair is wet.
During M.A.R.S./Cobra's first attempt to steal the warheads, Duke and the other soldiers on escort duty stand in a line to meet the attackers. Trained soldiers would have sought cover or concealment and returned fire from behind trees, disabled vehicles, and other terrain.
During the flashback to Duke's proposal, both Duke and Ripcord have goatees. While U.S. military grooming regulations are relaxed in certain circumstances, they would not have been allowed to have goatees at a formal gathering like the one they were at.
The nanomite warheads are said to be traveling at a speed of Mach 6, and for the Night Raven to have reached them in time it would have been required to travel at a speed well above Mach 6. Anything flying faster than Mach 1 is accompanied by a sonic boom, but neither the warheads nor the Night Raven are heard creating one.
At the beginning McCullen's ancestor has a heated metal mask sealed on his head as punishment and to be made an example to those who betray the crown. The mask is attached to McCullen's head while it has been heated to glowing hot. This method would've actually killed McCullen from the extreme heat killing of the nerves and muscles in his face or cook his brain and would not have survived this ordeal to complete France's plan to show what happens to traitors.
At the end of the fight for the arctic base, Cobra blows up the ice cap. Ice is then seen dropping through the water onto the base. Ice floats.
Although Scotland and France were allies in 1641, the charge against McCullen was selling arms to enemies of the crown, with no other specifics given.
The CGI tram ramming the Hummer during the Paris chase, loosely based on the Paris "Tramway des Maréchaux", looks nothing like the actual tram. The movie is set in the future; things change.
In Kyrgyzstan, Duke and crew head for Ganci. The United States Air Force officially changed the name to Manas Air Base in 2002 or 2003, in honor of a NYC Fire Chief who died at the World Trade Center on 9/11/2001. Official US policy dictates that only bases within the US are named after people, while bases overseas are named after local towns or geographical locations. That may not apply to older bases.
At the start of the movie, McCullen (a Scot) is accused of "treason" for selling arms to overthrow the king of France. French law allows "soldiers in the service of France" to be charged with treason. As an arms dealer to France, particularly at that time, McCullen could very well have been considered a soldier in the service of France.
When Ripcord jumps through the train in Paris, he has a perpendicular trajectory inside, as if the train is not moving.
In a flashback, Duke is almost in the doorway of a house when it explodes. He walks away with a few cuts. Later, when the ICBMs are launched, none of the Joes suffers any heat burns or effect of the thrust, despite standing a few meters away.
When Scarlett fights the Baroness in the invisible suit, the Baroness isn't wearing any gloves. When she turns on the invisibility, her hands disappear.
During the flashback of Rex' funeral, the ceremonial firing squad seems to be firing directly into the crowd of spectators.
The scar on Duke's cheek changes size throughout the film. It's quite long at the beginning, and a lot smaller at the end.
When the warheads are stolen at the G.I. Joe headquarters, Duke grabs an AA-12 shotgun, a fully automatic 12-gauge shotgun. When he shoots it, it sounds like an M16.
Young Storm Shadow knocks young Snake Eyes on his back as they fight in the kitchen. When Snake Eyes flips up to his feet, a grown man's grunt comes from the boy's mouth.
In the underwater chase, the camera eventually cuts to a shot of Duke from behind as he pilots the craft, and he says "I'm not lettin' those two get away." You can see Duke's reflection in the glass, and his lips are not moving.
While Rex Lewis was uploading the data on the nanomites on the computer inside the bunker, the keyboard he is using is a portable silicone gel model while the sound it makes is of a plastic keyboard.
In the underwater battle, when one of the SHARCs is hit by a missile, the pilot is flung out screaming. An underwater scream sounds very different from a scream on the surface.
During the scene in Paris, when the Joes are walked into the police station, you can see director of photography Mitchell Amundsen holding a camera on the left side of the frame.
In Tokyo, young Snake Eyes searches through an aluminum trash can. Japan has no aluminum trash cans; trash is put into latticed grilled dumpsters called "gomi-stations" or "trash stations".
During the East Africa flashback, immediately after the air strike, a snow-capped mountain ridge is visible in the background. While snow does occur at high elevations in Africa, in East Africa it only appears on peaks well inland, such as Mount Kenya and Mount Kilimanjaro.
The President's "American" accent slips back to Jonathan Pryce's native English accent several times.
While cleaning up "The Pit", just before Snake Eyes' 20-year flashback, one Joe sweeps trash into the shovel of a second Joe, who immediately dumps it on the ground.
Breaker immediately says he was "acting" for McCullen after the nanomites eat the neoviper in Paris, but he couldn't possibly know they weren't still watching through the button camera, so he would have given away that it was an act.
When Duke first meets General Hawk at the pit, he is called Captain. During the proposal flashback, he is wearing shoulder boards of a Major.
Early on, Destro says that "You've tossed the caber out of the park!" Caber tossing is judged on skill and precision, not distance. Tossing a caber out of the park would likely result in a very poor score.