Storm Shadow: I said I'd kill him if he touched you again.
The Baroness: I heard you the first time.
In the scene where Ripcord and Duke are in the transport and Ripcord pats Heavy Duty on the back and gets his arm twisted as a result, Ripcord makes a crack about Heavy Duty having a "Kung Fu Grip". This refers to some of the earliest G.I. Joe's action figures who were advertised to have the Kung Fu Grip. See more...
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Continuity: In the flashback scene where the younger Snake Eyes and Storm Shadow are fighting in the kitchen, Storm Shadow kicks the burners on on the grill as Snake Eyes runs across them. In the next shots, the grill is turned off to allow Storm Shadow to perform his leg lock choke hold just before the Hard Master walks in.
Continuity: When Ripcord is chasing down the warheads up high in the "Night Raven" plane, the heads-up-display indicates him being at around 65,000 feet. When he chases one down to Washington DC and is flying no more than 200 feet off of the ground, the HUD is still indicating an altitude of around 65,000 feet.
Other: In the scene where they are transporting the warheads with the Apache air escorts, just as Duke says, "I thought we were done with this conversation," about five and a half minutes in, there seems to be a passenger coach in the middle of the desert very close to the secret base. (They don't see or acknowledge it.)