Factual error: After killing the guards who rush in after he escapes from the stasis chamber, Storm Shadow looks at Warden James and says, "Welcome to hell". The ground he is standing on is completely covered in water from when the stasis chamber broke, spilling it everywhere. James uses this to his advantage and slams a defibrillator paddle onto it, electrifying the wet floor to shock Storm Shadow. James then gets up and takes off running... across the very same floor while Storm Shadow is still being electrocuted, but without a hitch.
Plot hole: When Storm Shadow busts out of the containment chamber in the prison, he throws two shurikens at some guards. Where did he get these? He came in in Snake Eye's full body suit of armor, but in the tank he had on the life preservation suits for the injections and aquatic suspension. If they prison had any ounce of intelligence and protocol at all for processing prisoners, especially ones as dangerous as a ninja and two leaders of a global threat organization, Storm Shadow would have been stripped and searched in full before put in that container. And there's no way he swallowed the shurikens.
Plot hole: Even if someone would make all nuclear powers launch their nuclear missiles and then destroy them you still wouldn't have a nuclear weapons free world as most of those nations have plenty of nuclear weapons in reserve. A lot would be even be armed and ready to go for a possible second strike.
Continuity mistake: Duke and Roadblock are having a contest to see who can shoot a cupcake at the end of a shooting range. In the shot from their perspective, there are some orangeish pink cross shaped targets mid range. The one on the far left is crooked and leaning sideways. But in shots from the cupcake's perspective, that same cross is standing straight up.
Continuity mistake: When Duke and Roadblock are playing video games in Roadblock's house, Roadblock's kids come up and start messing with Duke. They knock Duke's headphones off and comment about his big ears. But then Duke stands up with them on his back and his headphones are on his head again. The next shot, they vanish.
Continuity mistake: Following the title of the movie, the sequence that shows the Joe's file cards has all the Service ranks (not the first Rank line) from the toy line's ranks, instead of the movie's actual ranks. i.e. Roadblock's file card has the service rank stated as "E-7 Sergeant First Class" while he's holding the rank of Sergeant-Major in the movie, and Lady Jaye's file card states her service rank as "E-6 Staff Sergeant" while she held the rank of 1st Lieutenant and was promoted to Captain at the end of the movie.
Continuity mistake: Jaye drops some groceries in front of the Chief of Staff to lure him with her curves. As they are talking and she says, "Who says chivalry is dead, right?" she rakes her hair over her ear in one shot, but it doesn't stick and falls back in front of her face. In the next shot, it is suddenly raked over her ear and stuck there, at which point it falls out again when she moves.
Plot hole: Storm Shadow is disguised as Snake Eyes when captured. They still think he is Snake Eyes when transporting him to the prison. But he is still in his full body suit of armor. Doesn't really matter what prison you're going to, even so, this is the one for maximum security and houses Destro and Cobra Commander. It is not logical in the least for them to not have removed his body armor before even putting him in the prison transport, especially seeing as how easily his mask was removed when inside.
Continuity mistake: To escape the assault of attack helicopters, Flint, Jaye, and Roadblock jump down a well. it is night time, but the sky is bright orange from fire and explosions all around, even visible as Roadblock is falling down the well last. But when they surface from the water mere seconds later and look up, and there is only a lower blue light in the sky, where it was bright orange from fire moments earlier.
Continuity mistake: Duke pushes Flint out of the way as a chopper hits the Hummer he is next to. Duke is engulfed in flames. As Roadblock is seeing this, there is smoke all around him so thick you cannot even see 2 feet past him. Then only a moment later as he begins to run, the smoke/sand is all gone and you can see he is next to a vehicle.
Continuity mistake: After Mouse snipes the cup from an enemy solder's hand to cause a diversion, Duke and Roadblock rush off and get into a fight with two other Asian solders. Roadblock pins one against a vehicle and pounds his face with his heat gloved hands. The solder's hat comes off, but in the next shot it is on again.
Factual error: In the beginning scene, Roadblock melts through the fence using some high tech gloves. The design and application of these gloves make no sense realistically. For one, the gloves are open fingered, thus causing great risk to Roadblock of even just a melted metal drip with a slight breeze. The intense heat, even if directed down towards the fence metal, would still be enough, if able to melt through metal in an instant, to burn his fingers as well, even from behind. It would be much safer, much easier, and much more practical to have the same type of device as an external stick or long object, or even an extension of a gun, keeping the hands out of harm's way.
Visible crew/equipment: In the Best Buy extended action cut edition of the Blu Ray, there is an added scene at the beginning of the movie featuring Jinx and Snake Eyes training. Near the end of the scene, Snake Eyes jumps near a tree and the camera faces upward. When it does you can see where the dojo set ends, and you can see the top of the actual set with tons of lighting equipment on the ceiling.
Continuity mistake: In the scene when Roadblock drowns Flint he is holding Flint with his left hand and turns back to get a beer with his right hand, but in the next shot when Flint is shown struggling with his face in the water we can see that Roadblock is holding him with his right hand, from the thumb visible in shot.
Continuity mistake: After Firefly is killed and the Zeus launch is terminated, Storm Shadow hands Jinx the sword that Snake Eyes gave him to kill Zartan with. In the frontal shot, the wind is blowing Storm Shadow's hair out of his face completely, showing he is looking into the wind. But the next shot from a side angle, some of his hair is suddenly down over his forehead.