Continuity mistake: When Snake kills the wrestler he falls forward shoulders forward, next minute his arms are over the ropes, next minute his arms are in a different position again - quite active for a dead man. (01:16:55 - 01:18:10)
Continuity mistake: When trying to escape the gang on Broadway, Snake and the others are in a yellow station wagon they stole from the Duke's men. They turn the car around to back it through a barricade of cars to escape. One shot shows their car's head lights are on, but just before it hits the barricade, the headlights are suddenly off and then are back on again in the next shot. (00:56:55)
Visible crew/equipment: When Snake is back on top of the skyscraper to get to his glider you can see the elevator doors sliding shut behind him....and the fingers of the people pushing them. (01:19:50)
Revealing mistake: At the end when Snake drives over the hidden land mine and the cab is blown in half you can see three sets of wheels under the front half of the cab and a strange looking flap probably used to conceal them. (01:24:50)
Continuity mistake: When Snake finally stops the glider on the roof of the WTC, the nose of the glider sticks over the edge several feet but when the shot briefly switches to an aerial view, the nose is entirely on the roof. (00:27:35)
Chosen answer: During a mission known as the "Leningrad Ruse." He and his flight squadron were sent unknowingly on a suicide mission. During it, his goggles cracked and let in a poisonous gas, paralyzing his iris. He has to wear the patch because his eye can't focus against bright light, causing pain. This is mentioned in the novelization.
LorgSkyegon