Some ??? Monsters, such as Moo, have unsettling or non-standard designs, as do exclusive enemies, like Magma Heart, which is a dragon that looks like it's made of lava.
Wracky is a shout-out to the Child's Play series and is a living doll that wields sharp objects from Hammerspace. When you first get a Wracky in the mail, Colt thinks it's creepy and tries to throw it away, only for the doll to reappear the next week—and to unlock the breed as a species, you have to let a mosnter die. Their card data additionally says Wrackies are born from the grudges of dead monsters.
After you obtain the Joker Mask in 2, Master Pabs tries to wear it and gets it stuck on his face, unable to take it off, and it's implied if he kept in on he'd be possessed by the Joker inside the mask. They're only able to free him with a Gali Mask.
Jokers in general are terrifying, bloodthirsty, vicious monsters, especially in 2 where they're a Monster Clown. Occasionally, idle animations have them take off the mask, and the face underneath, which is different for every Joker subspecies, is horrifying.
One of the themes of Monster Rancher 4 is trainers using horrible methods to increase their monsters' strength. One such method is modifying monsters with rusty, ancient materials. One of your rivals eventually does this to his Golem to try and catch up with your hero. At first, he claims that Dodongo was perfectly okay with this; Rio calls him out, spelling out how Dodongo only went along with the painful procedure to make him happy. She strips away all of Gramm's illusions and makes him break down with horror upon realizing what he's done to his best friend.
Another one of your rivals runs his ranch by forcing monsters to run on training gadgets all the time, in tiny little pens. When he shows off his ranch, he brags about its efficiency, and how his ranch is on the cutting edge.
Rio has Blip Vert visions of an army of crucified Monsters in 4, which come out of nowhere and linger just long enough for the details and screaming faces to register.
Some attacks can function as a Jump Scare, like Suezo's Chewing, where it suddenly grows to an enormous size and chews on an opponent.
If your monster is severely outmatched by an opponent it can get injured, sick, or even die after a fight, making fighting any opponent with high stats extremely nerve-wracking if you have low life or defense.
In Episode 2, Holly berates Genki for thinking the problems Moo caused are like a video game. She reminds him that in this world, Moo is not a game and the destruction he caused was very real. Given what we learn of Holly's past in episode 8, where Moo's forces slaughtered her village, this sequence can be hard to watch.
Golem's Berserk Button being pushed in Episode 3; he slaughters all the Jells in a blind rage, even one that begged for mercy.
The death of Allan's Worm in episode 4. It has the life drained out of it, slowly, as Allan helplessly watches.
Tiger's introduction, where he mugs the heroes for their items and is in a position to easily kill Genki. He's described as The Dreaded for good reason.
Tiger's defeat of Captain Dino in episode 5 implies that he slit the latter's throat or chest open. Including choking noises as he dies.
Genki's nightmare in episode 8, involving him believing the entire series was All Just a Dream and being trapped under the sidewalk.
Holly's memory of Moo's attack on her village in episode 8. She steps out of the cellar and everything is gone; all that's left are remains of houses and Lost Disks.
Monol's story about the Monster Rancher world and how the ancient people of Pangea brought about their own downfall by creating Moo. Genki comments that things about that story remind him of his world. The last shot of the flashback is of a completely red planet.
Pixie:Disappear. [turns Captain Clay into a Lost Disc]
Ditto with Captain Scale Jell:
You're going to have to destroy that boy with your own two hands!
Joker ensnares the heroes in illusions so he call kill them easily. Tiger sees Moo, Golem thinks he's drowning, Suezo is distracted by female monsters, and Genki and Mocchi are chained up... and Holly has daggers falling from the sky at her.
Undine accidentally sets herself on fire, nearly burning to death. When Golem tries to save her, she refuses and jumps into the fire herself.
Gray Wolf's fight with Tiger turns very vicious towards the end, so much so that after the episode's initial run in English, some of the fight was cut from subsequent airings.
The gang finding remains of the Astros' space ship turned prison camp, including shattered lost discs, scrap metal that looks suspiciously like Astros, and broken prison chains.
The truth of the Pendant civilization, with the revelation that Monsters were created in test tubes. Colt's toucan, Joy, underscores this:
Joy: Born in test tube! Born in test tube! Squawk!
This ends up disturbing the characters. Mocchi asks Genki if he was born there, and Genki can't answer him.
Moo does a lot of nasty things, and what makes it worse is that he can't be stopped until the finale.
His shocking of Pixie in episode 47. In the uncut version he visibly chops her wings off, and shocks Genki as well.
Moo torments Holly over the destruction of her village and corruption of her father in episode 47. He comments that she must be filled with more hatred than anyone, and it seems he's right.
In a case of Bowdlerization making things more intense, Moo's beam attacks against the Dragon army. They're clearly hit, and in the uncut version they spiral to the ground like airplanes. By removing that, the dub implies they were vaporized on contact.
Moo going insane with hatred in episode 47. His rational side shatters, and he focuses only on causing as much death and destruction as possible.
Even worse, this is visualized by a scene of Moo's human form being strangled as his body is tied up by strands of darkness.
Moo pulls a very unsettling face as the Phoenix burns him alive in the uncut Episode 48. The animation for it is even worse, with his eye bulging and dilating.
Mum Mew's eye lasers.
In episode 73, after an entire season of lightheartedness, Moo (as a Ruby Knight) nearly kills Holly's father and absorbs Durahan and his gang to create its body. Then, Genki and the others journey into the heart of Moo's soul to finish him off. Not only do they see Durahan and his gang screaming in terror as the soul starts to consume them, it tries to possess the Phoenix as it nears defeat.
Mum Mew: [struggling with the evil soul] I don't wanna change! I like myself just the way I am now!