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)
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