* YouFailBiologyForever: The Pain doesn't seem that sure if his pets are bees or hornets. The two species don't exactly get along. Unless the strangled cry of "my HORNETS!" [[UnusualEuphemism refers to something else altogether]].
** There's also plenty of made up plants and animals: For example, there's no such thing as a Baltic Hornet (hornets can't make honey) and there is no golova fruit (although, it's based off of a real fruit called a jackfruit).
* YouFailGeographyForever: Good luck finding any tropical jungles ''anywhere'' in the former Soviet Union, not to mention the ludicrous variety of animals housed in it. The [[JustifiedTrope justification]] is that the animals were brought into the jungle from other regions by the scientists for research purposes, and the jungle setting is there mostly to trick people playing the pre-release demo.
** Despite the game saying it's a "jungle", it looks more like what's called a ''mixed forest'', which the Soviet Union did have, for instance the Caspian Hyrcanian zone in Azerbaijan. Also, there actually are pockets of lush forest right next to arid mountain regions in areas of Tajikistan (where the game is suggested to take place) like the Varzob region. The mountainous areas later in the game also resemble the lower ranges of the Tian Shan mountains in Krygyzistan.
* YouFailEconomicsForever: The Philosopher's Legacy consists of enough money to fight the Second World War ''five times over''. The economic repercussions of putting this much money aside and doing little with it, then ''losing'' it... Although the next game actually does deal with the economic repercussions somewhat.
* CreatorBacklash: Done to Raiden from the previous game. Zero devotes a long CALL to the fact that the Raiden mask irritates him, and the Raiden mask is used to pose as Raikov, the impulsive, despised and ill-tempered lover of everyone's favourite homicidal lunatic Volgin; Snake beats him up and hides him in a locker, with the option of actually killing him. This pleased Raiden's substantial HateDom no end. [[RescuedFromTheScrappyHeap He got better]].
** In the Secret Theater video "Metal Gear Raiden: Snake Eraser", Raiden goes back in time to assassinate Naked Snake/Big Boss and take the Main Character Chair for himself. He ends up, among other things, getting kicked in the face by Naked Snake during the HALO jump, and [[BlackComedyRape almost raped by Volgin]], mistaking Raiden for Raikov.
** The MetalGearSolid4 trailer also takes a potshot at Raiden, with the crowd booing heavily when he unmasks himself and his getting royally creamed by Snake during their fight for the main character chair.
* FakeNationality: British-born Neil Ross and American-borns Jim Ward and Grant Albercht voiced Russians.
* HeyItsThatVoice: It seems [[WesternAnimation/FamilyGuy Diane Simmons]] decided to become a reporter in Quahog after Big Boss killed her. Also, Volgin's Japanese Voice Actor, KenjiUtsumi, previously voiced Commander Red in ''Manga/DragonBall'' and Raoh in ''[[FistOfTheNorthStar Hokuto no Ken]]'', making it his third role as a military despot. EVA's voice actress, although her alias names her as Suzetta Minet, sounds a bit too similar to the voice actress of [[Disney/TheLittleMermaid a certain redhead mermaid in a Disney film]], although some fans think she may have also been Creator/DebiMaeWest even after an in-house interview confirmed that she wasn't Minet.
** Colonel Volgin, The Fear, and The Pain are voiced by G.I. Joe veterans Neil Ross, Michael Bell, and Greg Berger respectively. Michael Bell (The Fear's VA) was, amusingly enough, The Cobra Commander.
** Colonel Campbell's seiyuu provided Dr. Emmett Brown's voice in the Japanese dub of ''Film/BackToTheFuture'', [[ActorAllusion Time Paradox]] indeed.
** The Boss voiced [[WesternAnimation/ToyStory3 Bonnie's mom]] as well.
** Looks like [[VideoGame/ResidentEvil4 Jack]] [[JimWard Krauser]] may have had a brief stint as a Soviet researcher who developed the Metal Gear weapons line.
** In Japan, [[KikukoInoue The Boss]] is basically what happens when [[Manga/AhMyGoddess Belldandy]] [[TookALevelInBadass takes massive levels in badass]]
** [[AaahRealMonsters The Gromble]] and [[VideoGame/FinalFantasyX Jecht]] voice The Pain here in English.
** Raikov in English is TheFlash, and likewise Ocelot in English is [[GreenLanternTheAnimatedSeries Hal Jordan]].
** ''The Fury'' attacks someone he'll ''become'' about [[MetalGearSolid4 fifty years down the line]]. Talk about a mind screw.
* ScrewedByTheLawyers: Why the [[VideoGame/ApeEscape Snake Vs. Monkey]] mini-game isn't in the 3DS and HD versions. Sony Computer Entertainment created, and owns the rights to ''VideoGame/ApeEscape'', killing any chance the mini-game has of being on other consoles by default (though it doesn't quite explain its absence in the PS3 and [[PSVita Vita]] versions).
* ThrowItIn: Kojima wanted to use a piece of licensed music for the closing credits, and a colleague of his suggested he listen to the band stellastarr*. He misheard this as "Starsailor", and liked the track "Way to Fall", which ended up being used.