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. Scanning the crates with your camera before the X-ray pretty much proves that something is still alive in there. 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 whales that suddenly appear if you drive your hovecraft too far away from the game's "map", and also the one in space.
Just to show you that the game is not fooling around, the very first monsters you fight are children, trapped inside some creepy exoskeletons that drain their lifeforce to power up their attacks. Sure, as you break them up, you free the children, apparently unharmed, but you don't know that from the start.