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.
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.
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 Storm Shadow boards the plane in Paris, he is wearing all-white civilian-style clothes. While in the plane headed to the Cobra base, he wears his white ninja outfit, complete with swords. When he lands, he leaves the plane in his civilian clothes.
When Storm Shadow and Snake Eyes battle for the first time as kids, Storm Shadow hits Snake Eyes with a frying pan. As Snake Eyes supposedly gets hit, he does a back flip and lands face down, head towards camera. When you see him get up, he is on his back with his head away from the camera.
After Storm Shadow and the Baroness' Hummer crashes, blood flows from the top of her head. When the Baroness gets into the elevator, there is no blood on her face. Blood reappears on her cheek as she goes up in the elevator, and flows down her head again at the top of the building.
In the submarine, when Scarlett noted the advantages of a military base under the polar icecap, the shot switches between closeup on her to showing the rest of the team. In the closeup, her shoulder is behind the gold pole. In wider views, her shoulder is completely on one side of the pole as she leans on it.
When young Storm Shadow and young Snake Eyes fight in the kitchen, Snake Eyes runs across the stove as Storm Shadow turns on the burners. A few seconds later the burners are off, and Snake Eyes even throws Storm Shadow on the now-off stove.
During the attack on the pit, Duke tries to stop the Baroness and Storm Shadow from escaping. As Duke arrives, storm shadows hands are by his waist. The next shot we see of him, is hand appears by his head, lowering slowly. the next shot, his hand is down, even though it would have taken a few more seconds for his hand to reach this position. This continues until the end of the scene.
During the fight between Snake-Eyes and Storm Shadow in Destro's Arctic base, Storm Shadow's shirt it ripped of leaving a small piece of sleeve on his right arm and a large piece of sleeve covering his entire left forearm in far off shots. In close up shots, they are reversed.
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.
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.
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.
During the raid on the Pit, Duke holds the Baroness and Storm Shadow at gunpoint with a 1911-variant pistol. When the Baroness approaches him, he dramatically thumbs back the hammer. The 1911 is a single-action design (i.e. pulling the trigger can only cause the hammer to fall) and therefore, prior to his doing this, the weapon would have been incapable of firing. (The move would have made sense had Duke been using a double-action/single-action design like the U.S. standard-issue M9A1, because cocking the hammer would reduce the trigger pull).
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.
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.
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.
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.
Flipped shot. During the young Snake Eyes-Storm Shadow flashback, Hard Master has his yellow robe draped over his left shoulder and his beard sweeping to the right. When Hard Master says "[Snake Eyes] does not fight like [a weakling]" the shot is flipped with the yellow robe over the right shoulder and the beard swept to the left.
The goof items below may give away important plot points.
When the Destro's Arctic base is being destroyed, Scarlett and Breaker run from the control room. Scarlett's hands are empty but seconds later she is shown shooting a Cobra guard with her laser crossbow.
Destro's Arctic base is said to be located beneath the Arctic ice cap. This is confirmed by the presence of polar bears and mention of the 'northern route'. The Arctic ice cap is a very thin (10 meters at most), flat, loosely connected aggregation of ice plates, nothing you can build big structures on or in. Several mountains are in the background, even though the Arctic has no mountains. The Antarctic ice cap is several kilometers thick, above a rock shelf.
Scarlett suggests that Ripcord's aircraft needs verbal commands in the Celtic language. The Celts were a group of tribal societies that spread over much of western Europe; the original proto-Celtic language split into several different local languages. Proto-Celtic is a language that we can only attempt to reconstruct and we have no way of knowing what the actual words would be. There is no such language as "Celtic" and Scarlett uses the modern Scottish Gaelic words "cuir amach" (meaning "eject, expel, put out") and (presumably - it is difficult to say because her pronunciation is so bad) "tarraing" (literally meaning "pull, draw", in the context of the movie meaning "fire!" - probably because originally "fire, shoot" would have been done with a bow, which one has to pull back to fire, although the authenticity of this usage is not certain).