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. (00:02:35)
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. (00:05:20)
Continuity mistake: Jaye says, "We didn't. We did. Distinguished marksmen". As she does, Flint reaches towards her and Mouse is looking up at her. the next shot, Mouse is looking down. (00:08:10)
Continuity mistake: While after the first nuke, Flint pushes an enemy solder over a railing to plummet to his death. He falls face down, but in the next shot, he is falling face up. (00:11:15)
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. (00:13:30)
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. (00:20:00)
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. (00:20:45)
Continuity mistake: Warden James is giving "Snake Eyes" a tour of the prison as he is leading him to processing. They enter a room and James talks about the temperature: "kept to a crisp 68. Almost calls for a... a Snuggie". He is pointing to both the yellow tubes at the walls when saying the first sentence. But it cuts to a wide shot for the second sentence and suddenly his arms are at his side. (00:27:30)
Continuity mistake: Cobra Commander asks, "How's our former president?" Zartan says "Worth his weight in platinum". As he does in the wide shot, he turns away from the Commander and faces the nuke. In the close up following that shot, he turns towards the nuke a second time. (00:40:25)
Continuity mistake: While Roadblock is first talking to his brother on the street, one shot shows a group of people walking up behind Roadblock. A couple of shots later, that group has suddenly vanished. (00:43:40)
Continuity mistake: When walking through Roadblock's "old stomping grounds", Flint takes a plastic sheet off some exercise equipment and tosses it to the ground. The next shot from the front, the sheet is back in the air again and hits the ground a second time. (00:44:40)
Continuity mistake: As Flint and Roadblock are talking about how they have enough for a battle but not a war, Roadblock is inspecting a pistol with a large silencer/suppressor on it. He then sets it down on the table. The shot cuts to an overhead view, and that pistol has disappeared. (00:46:00)
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. (00:52:00)
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. (01:38:40)
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: 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: When Storm Shadow and Snake Eyes fall out the window while fighting, all the window pieces fall to the ground and nothing is against the wall. When Snake Eyes gets up, and when he throws Storm Shadow to the ground, there's a long piece propped against the wall now. When the two are rolling around, it's now gone.
Chosen answer: I believe three are named as Grunt, Clutch and Tunnel Rat in the script and credits.