* Look closely at the Fast Travel station in New Haven. If you pay attention to where it is located, it is outside the barriers that inhibit vehicle access to the interior of the city. Why would someone want to put that there? So in case bandits hijack the Fast Travel station, they'll pop in outside the barriers and city's defenders will have cover to gun them down.
* Given the very old story of Pandora's Box, is it any wonder that the Vault on Pandora was revealed to [[spoiler:not contain any loot at all, [[SealedEvilInACan but rather a universe-destroying thing from elsewhere?]]]]
* [[spoiler:When you open the Vault and have to fight The Destroyer]], Angel only mentions that you know where to hit it to kill it, which left many players confused since there was no previous hint of its existence. However any player who payed attention to Pandora's wild life should recognize that [[spoiler:the Destroyer]] has the same split jaw anatomy as the rakk hive, who in turn have their weak point on their eyes. This also means that the rakk hive might be biologically related to [[spoiler:The Destroyer.]]
* The fact that Commandante Steele doesn't use any Siren abilities [[spoiler: when you finally fight her resurrected, Claptrapped self in the 4th DLC.]] Sirens have a mystical quality: there are only 6 of them in the universe at any given time, with a new one coming into existence whenever one of the 6 dies. [[spoiler: It's likely Steele lost her Siren abilities when she was killed by the Destroyer, with her "place in the universe" immediately transferring to a new Siren. When you face her as Steele-Trap, her Siren tattoos are gone and have been replaced by Claptrap circuitry tattoo.]]
* The loot dropped from the Destroyer is of lousy quality, generally no better than what would be dropped by a regular enemy. There's just a lot more of it (most of which is just ammo). This is in keeping with the Vault being full of nothing except "tentacles and disappointment".
* The entire game, even series, seems to be a giant TakeThat against the idea of [[MegaCorp letting corporations act in a government's place]]. In the first game alone you have a corporation that literally abandoned a planet of people to mutated raiders and deadly wildlife, one that didn't even try to save lives during a zombie outbreak, and one that treated its best military commander with the same respect you save for a data entry clerk. We all know what happened with the corporation shown in the 4th DLC, which, as of the second game, had waged a war with the population for 3 years, turned into a Orwellian corporation full of backstabbing corporate climbers and run by a CorruptCorporateExecutive whose policies were on par with Stalin's regime.
* Why do human bosses reappear after a while? They can use the New-U stations to come back.
* The motto on the Welcome To Pandora billboards: "Your final destination, GUARANTEED!" Even leaving aside the implications from the [[Film/FinalDestination film series]] of the same name...