When the main villain Casanova rapes a girl. With a snake.
When he confronts a woman who we know has been taking self defense classes. Too bad he's been watching her and learned the counter moves. Especially the art of groin protection.
Cat and Mouse is particularly notable Nightmare Fuel, ending as it does with Pierce having flayed his skin off his body, exposing his organs. The narrator, being a doctor, literally can't believe the man's still breathing. And while we're at it, both Soneji and Smith. You could be taken down by them, anywhere, anytime, for a nearly random reason.
In Violets Are Blue Cross goes up against vampires. Well, not real vampires so to speak but evil murderers with fangs who drink blood. The way the vampires' lifestyle is depicted is pretty damn spooky, including various disturbing, and at times pedophilic, sexual acts.
I, Alex Cross is not as abundant of disturbing content as some of his other work, but when it does show up it is absolutely unnerving. The way Zeus is describes as a heartless bondage fiend, the character of Remy Wililams who lives out in the middle of the woods and puts his (usually young female) victims' corpses through a wood chipper, etc. What makes things worse is that both of the above got to one of Alex's relatives.