It gets even worse when you see it later on the M Disc and that music is playing.
The human trafficking in the factory and the slaughterhouses is frankly unsettling in and of itself, especially if you haven't figured out yet what the DomZ plan to do with them. Then they start abducting children. Heck, one young NPC disappears later in the game.
Then there's that business with the lighthouse. One minute, it's as you left it. The next time you approach it, however...
The way the DomZ monster deals with the Alpha Section who didn't neutralize all the intruders. There's no warning, no words spoken, no clear idea exactly what the thing is doing to him as he groans in agony. All we know is that, when it's finished, he hits the ground as a corpse and the beast turns its attention to Jade.
Crochax aren't particularly scary by monster standards, especially when you've whacked a few of them already, but they aren't half fast and they can reduce you to button-mashing if they attack in groups.
The appearance of the Pterolimax has shades of Nothing Is Scarier. At first, the Pterolimax are shown as two goofy faces with inane smiles on them, and after you cross a bridge to meet them, they play "peek-a-boo" when you try and photograph the pair. That bridge was its tail, and those two "faces" are its eyestalks.
The whales that suddenly appear if you drive your hovecraft too far away from the game's "map", and also the one in space.