When Snake finds the DARPA Chief, the chief tells Snake that Psycho Mantis read his mind in order to figure out the chief's detonation code. But when Snake talks to Kenneth Baker, Baker informs Snake that both he and the DARPA Chief have been fitted with anti-ESP nanomachines, and the terrorists tortured Baker to figure out his code. So how did they get the DARPA Chief's code? They didn't. The Chief Snake met was actually Decoy Octopus, a master of disguise, trying to trick Snake into telling them about another way to activate Metal Gear; Ocelot accidentally killed the real Chief in an interrogation. You'd Expect: Snake to figure out that the terrorists do not, in fact, have the ability to launch a nuke or at least ponder how strange all this is. Instead: Snake, even after seeing a psychic hallucination of what happened to the DARPA Chief before he arrived, and even after multiple people talk ominously about how the card keys he was given are a one-time-use thing, doesn't catch on, and proceeds to use those card keys to activate Metal Gear, since he THOUGHT it was active already but it actually isn't, and now it IS active. And he can't shut off Metal Gear because the keys only work the one time, and even if they didn't, Liquid climbs into the thing and starts shooting before he can do anything else.
Also applies to the people who created REX. Having built a mobile platform capable of launching a Nuclear Warhead, they then had to implement a way to arm and disarm REX. Arming the platform apparently requires the aforementioned pair of detonation codes, shared between two high-ranking officials. Disarming can be achieved with the use of three keycards, which is actually one keycard that can change properties under the right conditions. You'd Expect: That the far less secure Fail Safe keycard method can only be used to disarm the Mobile Nuclear Launch Platform. Instead: This single keycard, under the right conditions (themselves achievable by a single, unverified person), can be used as a toggle between Armed and Disarmed, with no way to tell which state you are activating at any point. As A Result: FOXHOUND are able to get Snake to activate REX using the keycard he was given, simply by pretending that REX was already armed.
Seal Team 10's Bravo Team are trying to stop Dead Cell from taking President Johnson. The Dead Cell member that they are facing is Fortune, famous for not having a single bullet hit her. They try to gun her down, but sure enough, the bullets just curve away from her. So you'd think: Bravo team would just realize that they are wasting bullets and run. Instead: They continue firing at her, even though it's clear all of the shots are missing. As A Result: Fortune, pissed off that Bravo couldn't kill her, blows them all up with her rail gun, thus delaying chances of Johnson's safety.
During the prologue mission, Snake learns that his mentor, The Boss, has defected to the Soviet Union. Snake is equipped with a tranquilizer pistol, which he has trained on The Boss, that apparently uses Instant Sedation rounds. You'd Expect: Snake would just shoot her when it became clear that she was doing a FaceHeel Turn. Instead: He doesn't. Worse, the only excuse that's given is that he didn't want to harm his beloved mentor, something the tranq gun wouldn't have done - he instead goes for CQC, which would have been much more painful for her if he wasn't completely outclassed.
Otacon is attracted to Naomi, the person who injected his most precious person andpartner of over a decade Snake with the FOXDIE virus. You'd Expect: Otacon to carry at least a bit of a grudge for that. Instead: He falls in love with her simply because she's not currently being a bitch to him.
At the beginning of the game, an assassin breaks into the hospital you're currently staying in, strangles your doctor, gets her hands on his gun, and points it at you. You'd Expect: Her to blow your damn brains out right then and there. Instead: She just stands there for 5 seconds not doing anything. The Result: Ishmael strangles her, lights her on fire, and punts her out of a window.
Nine years after the events of Peace Walker, Huey Emmerich decides to rejoin Big Boss, now running the mercenary outfit Diamond Dogs under the name Venom Snake. Upon his return, Snake, Miller and Ocelot make it very clear to Huey that he's very high on all their shitlists, due to their beliefs that Huey was responsible for the demise of Militares Sans Frontieres and the destruction of the old Mother Base. You'd Expect: Huey to realise that he's on very thin ice, and stick to working with Diamond Dogs's research unit (or whichever unit the player assigns him to) while not doing anything that might piss off either his old friends or the mercenary army he now lives with. Instead: He actively digs himself deeper on two separate occasions. First, he shows the child soldiers Snake rescued earlier how to operate Metal Gear Sahelanthropus, resulting in the kids fleeing the base and stealing the mecha. Then, he proceeds to cross the Moral Event Horizon by causing a huge parasite outbreak on Mother Base that forces Snake to execute several of his soldiers and staff members. Needless to say, this doesn't improve his standing with Snake, Ocelot or Miller one bit.
At the end of the Mexico level, the hostage-taking cutscene features some really boneheaded thinking on the part of both the scumbag scientist and Raiden.
You'd expect the scientist to: Avoid direct confrontation with the cyborgninjakilling machine named Raiden at all costs, booking it in the opposite direction and calling for security to escort him to safety before either sending another team to subdue Raiden or evacuating the lab entirely. Raiden hasn't found him yet, he has a clear path of escape that doesn't involve going through Raiden, and if dozens of military-grade cyborgs couldn't capture Raiden before, then an unaugmented middle-aged lab nerd with a pistol and some hostages isn't going to do any better. Instead: The scientist picks up the Villain Ball by waltzing into the room with a gun pointed at George's head while demanding Raiden's unconditional surrender. Sure, he could blow George's brains out if Raiden tries anything funny, and he's presenting Raiden with a Sadistic Choice by flooding the remaining children's cell with lethal levels of chloroform, but aside from his hostages there is literally nothing standing between him and Raiden's blade. He has no backup plan when it turns out that Raiden is willing to risk George's life to take him down, and thus ends up as Half the Man He Used to Be.
You'd expect Raiden to: Use his Absurdly Sharp Blade to cut open the glass the instant he sees the gas pumping into the children's cell, instead of uselessly pounding on the glass with the palms of his hands until the scientist shows up with George as a hostage six seconds later. Once Raiden misses that chance, you'd still expect him to either (A), break the glass anyway and count on the scientist knowing better than to kill his only bargaining chip—which even in the worst case could save multiple hostages' lives at the cost of one—or (B), tell George to jerk away from the gun (or let George do it on his own initiative) and use that momentary opening to neatly decapitate the scientist before he can get his gun back on target. Even if a normal human under such pressure might not have the reflexes and precision to kill the bad guy instantly without hitting the hostage in the process, Raiden has already demonstrated such superhuman speed and control with his cyborg body that this ought to be possible for him. Instead: Raiden vacillates and wastes precious seconds for the children in the gas chamber by listening to the scientist's Evil Gloating, and when he finally does decide to choose George over them, he wastes the unobstructed shot at the hostage-taker's head (or alternatively, the arm holding the gun) that George gave him by jerking downward, and instead chops right through George's midsection to get the guy behind him, permanently maiming and almost killing George because he either Forgot About His Powers or just didn't care. Even worse, Raiden's team doesn't think to criticize him for unnecessarily cutting the boy in half, leaving them with no choice but to put George back together using cybernetics!