Vampire: The Masquerade – Bloodlines. As in many western RPGs, there is a Haggle skill that can get you better prices in stores. But what use is haggling in modern-day America, where prices are fixed? It seems silly until you realise that every single "store" in the game is one where haggling would logically be permitted. You buy things from a pawn shop and out of the back of a truck. Even the petrol station's gear is being sold "unofficially" by one of the employees.
A fine example is examplified by the Voerman sisters. Therese, who claims to have sired Jeanette, is acting in a manner completely different from her sister and childe, acting in a typical Ventrue manner and personality while her sister is anything but. Then it is revealed that the two are actually two distinct personalities of the same person, who turns out to be Malkavian. This also justifies how the two personalities fit into the stereotypes of two completely different clans in spite of the fact that one sired the other, in that she obviously has a few screws loose to connect the two personalities under the same bloodline.
Also, there's a good chance the player will realize the Stealth Pun at work before the Player Character brings it up in dialogue: the Lunatics [in this case, a nickname for Clan Malkavian] are running The Asylum.
While the were-shark quest may seem to come out of nowhere, by the book canon, it is surprisingly through and plausible. The wereshark is a Same-Bito, a hengeyokai variant of the Rokea (weresharks). Same-Bito, unlike regular rokea, have taken time to try and adapt to the life on the surface. Hengeyokai also are far more likely to deal with Kuei-Jin on neutral terms, unlike western shifters and kindred.
Why does LaCroix insist that you look at him when you tell him that you saw Nines Rodriguez leaving Grout's mansion? Dominate requires eye contact, and the Prince wants to be absolutely sure he's getting the truth of the matter.
The Elisabeth Dane, a ship where the Ankharan Sarcophagus was discovered had all it's crew slaughtered before the rest of the plot happened. The endings in which you discover what is in the sarcophagus seem to come out of nowhere unless you remember that Jack used to be a pirate. Yes, that, turns out to have been an actual hint.
The entire Malkavian route is full of Fridge Brilliance, because a good part of the story is hidden away in the twisted conversations before anything happens. In theory, you could know the outcome very early just by paying careful attention to the dialogue. Also, the weird "tuna-joke" the newscaster tells a Malkavian player? It's exactly what is happening, and might yet happen. Even the chess-motif is similar to the mail you get.
Why are VV's poems so terrible? Because, even though she's a Toreador who appreciates beauty more than other vampires, she's still undead, and most of them have lost the creative spark in the Embrace. Or maybe it's because she's a stripper, not a poet.
Why does Grout take so long to develop the madness of his clan? Answer, he doesn't. Later mentions of hearing voices are separate to his true insanity, which is his "infatuation with reason" as he puts it.
There's a further layer of fridge brilliance there: what could be the greatest possible madness to afflict a Malkavian, who have incurable insanity as their hat? Being absolutely convinced that he is the Only Sane Man, of course. This leads to yet another layer of fridge brilliance regarding the voices he hears: so far from being random babblings, they are a fine example of paranoia-as-heightened-awareness - truly an ironic affliction for someone who believes himself to see the truth more clearly than anyone else. The final layer comes when one realizes that even this heightened awareness was a falsehood - the greatest danger to him came from Ming-Xiao, not LaCroix.
So, there are Werewolves, notorious for their hatred of vampires, that are hanging out in Griffith park? Why haven't they attacked the city before now? Especially when an Antediluvian is about to rise? Answer: The sarcophagus contains only explosives, and the werewolves, with their spiritual powers know that. Hence, they have more important things to do then mess with a few vampires in a city.
It seems strange that a blundering security guard like Chunk should land a high-profile job as the front desk guard of the Venture Building right after screwing up his last job, until you realise that his sole purpose is to be a disarming figurehead for anyone wondering if there's something sinister going on in the building. The front entrance is filled with cameras, there's a small army of heavily-armed guards, a dozen powerful vampires past them, and finally the Sheriff if anyone should get past all that. Chunk's sole duty is to just sit there and look humorously incompetent to throw Hunters off the trail.
In the first bounty hunter quest, if Gimble had already captured McGee and cut his arms and legs off, why was he still trying to reach him at the tattoo parlor?
It's likely he'd bugged the parlor and wanted to drag in more victims (like people looking for McGee) by using the phone to contact them.
Also, are we really sure he did get McGree? I don't remember them actually saying it.
Gimble did get McGee; Carson mentions that Gimble has been mutilating both him and McGee, and after the boss fight with Gimble, you can look in one of the cells and see McGee's corpse.
A more serious problem in the same quest. Being able to send Gimble to Vandal in the blood bank is a great idea, but why doesn't it make you lose humanity? OK, Gimble is a serial killer, but when the mentionned dialog option appears, the player character is talking with Gimble in his waiting room and it is the only oportunity to do it. You discover the proofs that Gimble is a serial killer after this point, when you explore his basement (and speaking with him is no longer possible). You just sent to his death someone you didn't have any reason yet to suspect, so it should have triggered a humanity loss.
I had already figured out what Gimble was up to by that point, so maybe the game assumes that everyone did?
You just have suspicions, not the slightest proof. And more, much later in the game, there is another quest (the Wereshark) in which you can skip the boss fight by attacking and killing the main suspect when you just meet him... which this time costs some humanity.
During the tutorial, at the sequence when Jack teach the player character how to feed from rat blood, a Ventrue player character answers that his/her clan is unable to feed that way. The problem is: how could a just embraced neonate already know this? His/her first contact with kindred society happened less than a hour ago (the opening cutscene) and still lack most of basic information about the kindred societies.
You gotta remember, clan members tend to pick people like other members of the clan when embracing. Since most Ventrue are high and mighty and a lot are like that before being embraced, the PC could just be recoiling at the idea. Possibly said Clan as instinct?
This, and also that Lacroix and/or one of his vampire goons could've given you a very brief debriefing on your clan offscreen.
A minor one, but still: Lacroix, a former soldier of Napoleon's armies, speaks with a british accent during the whole game... Except any british native person, or anyone acquainted with one, could tell you that this really is nothing more than an fake accent (basically, the words are pronounced in a "british" manner, without the right diction or rythm). Why would they do such a glaring mistake, in a game with otherwise flawless dubs, instead of just hiring a british voice actor?
Well, one way to see it: the defining idiom of Lacroix is that he is a massively pompous Ventrue jerk. And what better way to hint that than making him talk with an imperfect british posh accent?
Alternatively: He learned English in England, but enough of his original French accent remained, and enough of the American accent he is currently immersed in snuck in, to make his accent sound "fake".
Very few people, especially those who have moved around a lot, have perfectly identifiable accents. This goes doubly when it comes to languages not native to the speaker. Figuring out someone who has never left Birmingham is from Birmingham by accent alone is one thing, but try figuring out the accent of a Frenchman who learned English from a German teacher at a school in Belgium, listens to British audiobooks and watches American TV.