Character mistake: When Guile promises to rescue the hostages while on camera with Bison he makes a point to mention Charlie by name to reassure him that he wasn't forgotten. Anybody who was in charge of a major recovery operation would know better than to mention a specific hostage that isn't already well known to the enemy because he just put a target on that hostage for further abuse. This was promptly shown in the following scene when Bison picked out Charlie to be transformed into a beast as a result of Guile identifying him as a personal friend.AD
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.
Other mistake: I know most goons in movies are bad shots, but this is stupid. There are at least 20 Bison Troops in the room. There is one Guile. The guards have machine guns, while Guile has a handgun, with only 1 or 2 clips. Yet these troopers all miss him, even the ones on higher levels of the base, which give them a far better view of Guile.
Deliberate mistake: Vega's claw never actually hits any of the furnace buttons, but it opens up anyway.
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.