Nightmare Retardant: Not the mod itself, which managed to make Houndeyes terrifying. In Sven Co-op, it's a popular server, but obviously, having a buddy with you mowing down hordes of twitchzombies lessens the impact a bit. The official server works to make this less effective (players are often split up and cannot speak to each other unless near each other, they bleed out when on low health, and ammo and weapons are as scarce as ever), but the snark of your fellow teammates and your laughs at their anguished screams kinda dumb it down a bit.
Originally, there were supposed to be zombies with big white eyes. They did not look frightening as much as just weird, and were cut.
The song in the game files labelled "shootrob" uses a similar Heartbeat Soundtrack with low growling in the background. Use an external program to speed it up and it sounds like, presumably, Andreas Ronnberg going "waowaowaowoowaowaowao."
Porting Disaster: In contrast to Cocyx's excellent port of the Director's Cut to Sven Co-op, someone else ported over the original version of the mod, and... didn't do as good a job. The unique weapon models aren't there, leaving unfitting models for the weapons. The skybox clashes with the lighting color. And, after turning off the power to open the power lock door, the additionally spawned enemies don't do anything and can't even be killed, to the point that one of them blocks the way out, thus making it Unwinnable without admin commands. Even more unwinnable situations can occur such as the gate that comes down past the turnstiles in the subway blocking respawning players, something Cocyx avoided in his DC port.
That One Level: The Hospital after the blackout. People tend to quit playing the game when they get lost too much. Made especially jarring by the fact that it's the first level.