* DemonicSpiders: The Golems due to their speed, hard hitting attacks, and high HP. Some of them can even cause Poison or Paralysis on you to boot and in certain areas, you fight more than one Golem at once. Nightmare Mode makes ''every'' encounter demonic spiders due to Aya's massively decreased HP and defense.
* FakeDifficulty: Square tried to make ''II'' more like the ''Franchise/ResidentEvil'' games, but with [[CameraScrew worse camera angles]] and an absolute lack of a quick, 180-degree turn. Many cheap shots and deaths will ensue. The original game generally favored more isometric viewpoints that, shock of shocks, showed most of a room without any awkward and abrupt angle transitions.
* FridgeBrilliance: If you examine Bowman's bed several times, Aya will note that there are clumps of hair on the pillow and foul-smelling stains on the sheets. Hair loss and altered body odor are both common side effects of chemotherapy, which goes a long way towards explaining why Bowman was eager to volunteer for the experiment.
* GeniusBonus: If you actually know what "Neoteny" means, a bit more of what the cult is trying to do makes sense. Well, as much sense as the intentions of a cult usually make. Neoteny is a term referring to an "adult" lifeform, showing traits from a younger form (the classic example being the axolotl; a species of salamander which retains the fins and gills which most other species of salamander lose after growing out of their larval stage). So basically, the cult is trying to "revert" humanity into more primitive forms in order to "reboot" humanities evolutionary process (somewhat ironic, given some researchers argue that a lot of the traits that set humans apart from other primates are neotenous).
* {{Narm}}: A lot of the [=ANMCs=] have really goofy looking faces for such hideous monsters, possibly because they look somewhat human from the transformation.
** The fat ANMC[=s=] and the aquatic ones make a silly "Ohh" noise when they are attacked or attack, respectively.
** Many people also seem to agree that the horse-like sound the creature the young woman at the Akropolis café transforms into effectively ruins the scariness of the scene.
* ParanoiaFuel: The Stalkers are chameleon-like monsters with an InvisibilityCloak. Unlike other monsters in the game, they can't be seen if they are in a room. You will only know if they are there if you suddenly enter the battle screen to a very loud, unnatural screeching noise.
** Knight and Bishop Golems are even worse. You don't detect them until they attack you, and they always land the first hit.
* TheyChangedItNowItSucks: Squaresoft tried to make it like ''Franchise/ResidentEvil'' a little too much.
* {{Tearjerker}} If you take too long in the fight against the Burner boss, [[spoiler: Mr. Douglas' dog Flint dies]]. [[YouBastard It was your fault, because you took too long killing that thing.]]
* UncannyValley: Most of the [=ANMCs=] in the game are animals with vaguely human-like characteristics. 'Strangers' are Ostrich/Dinosaur-like things that can mimic corpses and 'Chasers' are basically camels with horrifying, polygonal human faces. Their subspecies 'Mad Chasers' fall on their backs and ''start laughing'' when Aya attacks them.