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.
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.
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.
Gali proves to be Not So Stoic when he whips up a hurricane of sand to kill the Searchers, all because Genki cracked his mask. He goes ballistic and turns into a whirlwind while screaming that he'll destroy everything.
Undine accidentally setting herself on fire, nearly burning to death. When Golem tries to save her, she refuses and jumps into the fire herself, dying.
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.
This face◊ Moo pulls 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, when they fight it, 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!