* In the [[NamesToRunAwayFromReallyFast Bloodsucker Village]] in [=SoC=] a small shrine is set up, with a fire in the middle and some dead stalkers and heads on sticks scattered around. The thing is that Stalkers don't stay long in that village, much less do anything more than to tell people to avoid it. Which only lets one possible builder open.
* After the events of ''Clear Sky'', virtually the entire Clear Sky faction vanishes from the face of the earth. They're never mentioned in ''Shadow of Chernobyl'', and are given an oblique reference in ''Call of Pripyat''. Only two Stalkers you encounter are confirmed to be former members: Nimble, who goes from exhausted rookie Stalker to [[DistressedDude rookie Stalker in need of rescue]] to [[TookALevelInBadass master]] [[ArmsDealer arms dealer]]; and Novikov, who disappears after Clear Sky and reappears working as a technician for the [[BadassBookworm Ecologist faction.]] Doesn't seem like too big a deal, until you realize that the [[BrainwashedAndCrazy Monolith faction]] had a surge in manpower ''right after the events of Clear Sky''.
* Vodka in ''Call of Pripyat'', if not taken properly, can starve you to death. It's possible that the developers were trying to implement Korsakoff's Syndrome into the game, albeit in a rather fuzzy way.
* Despite the common knowledge being "the Zone gets more and more dangerous as you get closer to the CNPP," the northern areas of the Zone (those appearing in Call of Pripyat) are ironically less dangerous than the southern area (from the previous two games), taking Pripyat as the relative midpoint. Zaton and Yanov have fewer bandits, fewer mercs, virtually no Monolith presence outside Pripyat itself and less in the way of roaming hostile wildlife (although what wildlife there is tends more towards DemonicSpiders or BossInMooksClothing than GoddamnedBats). Monolith's relatively scant showing can be chalked up partially to the massive hit Monolith took at the end of ''Shadow of Chernobyl'', but the rest doesn't make much sense.
* The stashes. When you first start playing the game and find PDAs pointing you to loot containers on the bodies of people you just filled with lead, it seems like a very gamey mechanism to get you to trek around and provide you with progressively better gear. After all, why wouldn't that guy have all that handy stuff on him ? Then as the game goes on, you start getting overloaded with ammo that you're not using right now but might need later, guns and armor that are too nice to just sell (esp. in the first game where you can't repair them), med supplies that you'd be happy to have back after a heavy fight empties your stocks... and that's when you start stashing stuff all over the place like a crazed squirrel yourself, just in case. Congratulations, you're like a real stalker now!
* The lack of the Brain Scorcher in ''Clear Sky''. In [=SoC=], you deactivate it and only then does the northward exodus begin as hundreds of Stalkers rush towards Pripyat and the CNPP. In ''Clear Sky'', you just head north without even a mention of any psychic barriers in the way. Why? ''Because they hadn't been put up yet.'' The ease with which you and Strelok and an entire flipping faction of Stalkers penetrated the center of the Zone prompted C-Consciousness to put up the Brain Scorcher.
** Um, no. At the beginning of ''Clear Sky'' it's brought up multiple times by Lebedev that the Brain Scorcher exists and it's a major plot point in both games that Strelok and his group had found a way past it. It's the reason why the Zone was beginning to go unstable in the first place: it didn't want anyone to know the way past the Scorcher, and was releasing emissions in the hopes that one of those emissions would kill off Strelok's group before that knowledge spread. The first game also mentions that the Brain Scorcher is only one of multiple defense systems the Zone had put in place to prevent entry to the center. The more likely explanation is that Strelok and his group had merely found a gap in that defense system in that tunnel you see Strelok go into in the Red Forest, and in the nearby town of Limansk.
* Sometimes the damage detection can get a little bit...finnicky, to the point that an entire magazine of 9x19mm rounds to the chest won't do much more than piss that Ukrainian military trooper off. However, this can be rationalized (or [[HandWave handwaved]]) by simply assuming that most of these guys have artifacts on them that are simply destroyed or damaged when you finally manage to put them down.
* The labs, the behavior of the wildlife, and the experiments all tie together once you start fishing around in lab X18. In one of the side rooms, you can find (thankfully empty) versions of the tubes you see the PC being placed in if you join C-Consciousness at the end. On the opposite wall are cages holding dead Zone wildlife. Granted, all of this will be long before you've seen anything but vaguest hints about the true nature of the Zone and it's origins, but on a second playthrough it's absolutely mind-blowing.