These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Mantis' persistant refusal to believe in the existence of ghosts (despite great evidence to the contrary) became even funnier after the release of Metal Gear Solid 4 where Mantis appears...as a ghost.
Possessing a girl, even!
In #445, Liquid tells Otacon to program REX to accept any projectile on its rail gun, including a nuclear warhead. When asked why, he says that it's so REX would able to shoot down asteroids. In Metal Gear Solid 4, it turns out that JD, the main Patriot AI, was housed in a US military satellite orbiting the Earth disguised as debris, and Liquid Ocelot planned to use REX's rail gun to launch a nuclear warhead at it so he could use GW to take control of the entire Patriot AI system.
According to Hideo Kojima, Liquid really does have a horrible grasp of genetics.
And this strip and some earlier nes make mention of Big Boss writing an autbiography. Big Boss (in Liquid's body) lets slip about his fight with The End and tries to cover by claiming he read it in his memoirs which he then claims are on Amazon. Come MGS4, and apparently Big Boss' memoirs (Or at least the Snake Eater mission) are now declassified.
Chris guessed in one strip that the reason everyone says "la-li-lu-le-lo" instead of "The Patriots" is because they are all been brainwashed into being incapable of saying "The Patriots" as a phrase and a mental override always made them say that instead. Turns out that was in fact the canon reason.
Maybe Kojima is just taking stuff from the comic, because he's either bored or pissed that, unlike he planned, he can never just leave the franchise to his employees.
Magnificent Bastard: Despite early appearances to the contrary, Ocelot is still one of these here.
Mantis: But it's all about the little details! I mean, you must spend every day pretending to act like you're falsely letting on that you aren't not unbetraying someone you don't not purport to allegedly work for but really do! How do you keep all this shit straight without having an aneurysm?
Ocelot: * shrugs* Practice.
Saladin (Big Boss) is almost certainly one of these too, with his extreme fondness for plans, especially when it comes to manipulating Liquid. Not to mention his general badassery.