in MGS4, during almost every cutscene it shows Snake holding the operator instead of whatever gun you have out.
This could easily be forgiven if not for the fact that it SWITCHED A RANDOM WEAPON SLOT FOR THE OPERATOR so that once the cutscene was over, you'd have the operator equipped and lose one of the guns that was in your inventory before. This meant that after every cutscene you would have to go into your menu and swap it out for the one you wanted
especially annoying for boss fights as you have to do this every time you die -_-
I never ever used the operator (tried to limit my number of kills plus there's way better guns)
EDIT:
Also the same person who voices Revolver Ocelot also voiced Elroy Jetson

try unseeing that.
semi-related: whenever they're talking about "genes" in the mgs series (as they often do lolol) i like to imagine that they're actually talking about "jeans"
watching snake and liquid argue over who got the better jeans is priceless.