Continuity mistake: In the scene where Dhalsim changes the programming, all the computer shots of Blanka show him with normal skin, despite that it's turned green.
Continuity mistake: When Vega ambushes Ryu in the locker rooms, he just puts his mask in front of his face. Ryu kicks him right afterwards, and the mask rests solidly on Vega's head.
Continuity mistake: When Guile infiltrates the base, he has as his only weapons a pistol and a couple of knifes. But when he fights the Bison troopers in the control Center, he suddenly has a Heckler & Koch MP5 submachine gun. He does have the magazines when he enters the lab, but the submachine gun is fairly bulky and thus should be visible when he comes in.
Continuity mistake: When everybody prepares to bail out of Bison's base, Honda and Zangief are still locked in combat; Zangief is wearing an undershirt. But when Honda breaks away, the shirt is suddenly gone, and there is no indication - including tatters - that is was ripped off during the fight.
Continuity mistake: When Sagat and DJ first open the container full of Bison dollars you can see inside as it isn't full to the top, yet when it cuts back to them for a second time the container is full to the top.
Continuity mistake: When Ken asks 'Why are you making me watch this?', he is facing left, even though in the next shot Sagat is on his right.
Answer: In his fight with the guard, Dhalsim gets knocked into some chemicals. This presumably changed him. This is also likely the explanation if he had to do any signature moves from the games, which thankfully, he doesn't.