In the book are many scenes they cut from the film, such as the "Tale of El-ahrairah and the Black Rabbit of Inlé", which Hazel tries to avoid having told just before their Impossible Mission because it'll demoralize, i.e. scare the crap out of, everyone concerned. Bigwig insists on hearing it, though, and so we have to listen to how El-ahrairah descends into the rabbit equivalent of Hades to confront Death as a last resort to save his besieged people. El-ahrairah gradually loses his whiskers, his tail and his ears to the Black Rabbit in futile bets, then in total desperation jumps into a well of deadly plague germs in order to carry them back to the enemy — but it won't work, as the plague is carried by fleas nesting in rabbits' ears. Finally, the Black Rabbit agrees to El-ahrairah's request simply because his persistence in remaining alive is disturbing the place of the dead. So he sends mysterious demons to terrify the enemy into submission...
"...And that is why no rabbit who tells the tales of El-ahrairah can say what kind of creatures they [the enemy] were or what they looked like. Not one of them has ever been seen, from that day to this."
Just about every one of Fiver's visions, Bigwig's encounter with the Shining Wire, and the poisoning of the Sandleford Warren, to name a few. The film tends toward either short and surreal (the visions and flashbacks) or realistic and gritty (all the violence portrayed in the present tense), while the book has longer descriptions. Pick your poison, and know this stuff can be disturbing to more than just kids.
When Bigwig calls Hyzenthlay up to his burrow, her initial response is hauntingly similar to a sex slave. "If you want a doe you can have her, and no one is allowed to stop you" takes on a horrible new tone.
To the Efrafa rabbits the fact that Bigwig isn't the chief is one, due to the assumption that somehow there is a rabbit bigger and more badass than Bigwig out there.
The sequel, Tales from Watership Down, feature several new El-ahrairah tales that feature out-and-out Eldritch Abominations, from a predatory Elder Thing in "The Story of the Comical Field" to a monster beyond time and space in "The Three Cows" to something only seen in gibbering insanity in "The Hole in the Sky." Even a couple of the non-Eldritch Abomination tales are nightmare-inducing: "The Terrible Hay-Making" features a massacre even worse then what took place in Sandleford.
The animated film version
Yes it's a U-rated film (or G-rated, if you're Americannote in Germany, it has a 6+ rating, meaning kids over six years old can watch it, though a PG rating would suffice for something like this, and Germany doesn't have a proper PG rating. It goes 0, 6+, 12+, 16+, and 18+), but the movie is very disturbing and does raise questions of "How is this appropriate for children?" and "Why do people think this is for kids just because it has bunnies in it?" Some examples include:
Bigwig almost choking to death extremely graphically and realistically is horrifying.
The flashback to the gassing of the warren, with the glowing-eyed rabbits crammed into the tunnels clawing each other, trying to get out of tunnels that only narrow and spiral into dead ends. Holocaust parallels, anyone?
Holly appearing to tell the rabbits about it. The first the rabbits and the audience hear of him, he is moaning, "Zorn, zorn!note Translation: Destroyed, destroyed! Bigwig, Bigwig!" Bigwig immediately assumes it's the Black Rabbit of Inlé, until Holly drags himself to the edge and falls into the ditch they're in, completely battered and moaning, "All zorn!" We don't know who did this to him, until Holly tells the rabbits of his time in Efrafa.
Fiver's vision at the beginning of the film is terrifying. The music that plays during that scene does not help at all.
The rats that attack the rabbits while they're sleeping in a shed.
Cowslip's warren. It's a nice little place with good food and shelter, but then the leader does some creepy rambling about the Black Rabbit. Turns out that the warren is near a farm that leaves the food in order to fatten and trap the rabbits.
Near the end when Woundwort attacks the dog, if you're watching on YouTube, pause at the right time and Woundwort will look like something out of your worst nightmares.
The dog isn't exactly a sweetheart either, rising up from the ridge with a mangled bloody Efrafan bunny in its jaws.
The disturbing parallells between Efrafa and Nazi Germany - or any fascist state.
Blackavar stays behind in an attempt to stall General Woundwort only for him to easily swat him down and tear out his throat in an extremely graphic manner.
The Animated Series
The children's series might actually do a better job of foreshadowing the true horror of Cowslip's Warren than the movie version, partially due to the way everyone just sort of...lets themselves forget about their search for Pimpernel, easily distracted by the readily available flayrah.
The show doesn't focus much on the horrified realization of what the warren of the shining wires truly is (because, after all, it's aimed at a younger audience) but imagine it from Holly's perspective. Pimpernel was weak, couldn't travel on...and this warren was big, and comfortable, and welcoming, so he left his friend in their care. Just for a few weeks. And then he comes back...
The realization of the true depths of this version of Cowslip's insanity. While in the novel and the movie adaptation Cowslip is mostly a sad, spiritless character, living with one foot in the grave and sending innocent newcomers to their deaths to postpone what he knows is the inevitable, the series portrays him in a way that gives the audience chills.
In later seasons, as the plot decays, Cowslip becomes a sly, cruel schemer; in the first season, which started out more or less loyal to the book, Hazel And Company realize as they're leaving that living under the shining wires has driven Cowslip completely and utterly mad.
Hazel: Come with us. You don't have to surrender to the shining wires!