The spooky atmosphere of the scene aside, the egg that hatches at the start of the film is even larger than the full-sized human baby it contains. Considering a normal-sized human(oid) gave birth to it... that had to hurt. Even more so if they lay eggs through the same place reptiles do.
Daniella and Daisy's kidnappings are played to scary effect, as Iggy and Spike grab them when they think they're safe. Daniella's kidnapping is worse because it happens just after Mario leaves and her screams are cut off when they gag her. Worse, Iggy and Spike had been kidnapping other girls off-screen, and the residents of Brooklyn have no idea who took them and why.
Koopa attempts to seduce Daisy in an incredibly creepy manner, talking about how fresh and clean she is while telling her she really belongs in the world of dinosaurs. His appearance gradually gets less human over time, including a more prominent forehead and a long lizard tongue, and when he moves in to kiss her Daisy, understandably, screams and forces him away. (Early drafts suggest he was attempting to rape her.)
The brothers dissolving between dimensions. Mario was conscious of the fact that he disintegrated, and there's a lengthy shot of him falling between worlds without any solid ground above or beneath him.
Koopa's Transformation Ray, which can de-evolve his prisoners into their evolutionary ancestors or worse. When the machine is first seen and activated, Toad's head is shoved into it, where his face is repeatedly stretched and grotesquely warped out of shape as the rays rewrite his DNA into a Goomba's. Toad's screams of agony make it very clear that this process is not pleasant.
Made even worse in the deleted scene where a technician gets devolved into primordial slime and sloshes out of the chair and onto the floor. As Koopa puts it, "it's more than just death—it's being... undone". The reason Koopa had the guy devolved: He sneezed. We get that Koopa is a germaphobe, but it kinda makes you wonder how many people he had slaughtered for even the slightest "infraction".
Halfway through the movie, Lena is fed up with Daisy and Koopa's interest in her and attempts to kill her with a knife. Daisy is barely able to stop the blade from going in, and when Yoshi rescues Daisy by grabbing Lena with his tongue, she retaliates by stabbing him in the neck and getting away. It's very intense, especially for kids, and is made worse by the Mood Whiplash of jumping back and forth from this scene to a funny scene of dancing Goombas in the elevator.
After Yoshi helps Daisy escape, she runs down a hallway and into Toad the Goomba, who is shot by another Goomba's flamethrower and set on fire. Daisy is horrified, and it's made worse by the practical effects used and that despite being turned into a mindless brute Toad is clearly in pain and scared.
After Lena succeeds in reuniting the meteorite piece with the meteor, energy flows across her, briefly showing her skeleton. Then she's suddenly flung into the wall and disintegrates into a skeleton, literally fossilized by the meteor energy.
When the Bob-Omb blows up, Koopa is already half de-evolved into a dinosaur by this point and looks very freaky as he has claws, a reptilian head, and a too-wide mouth with More Teeth than the Osmond Family but still retains a humanoid body. When he's launched into the bucket, there's a very effective pause as all you can hear are faint rattling noises, before a sudden Jump Scare of his Tyrannosaurus form lunging out, its mouth filling the screen.
After retrieving the meteorite at the night club, Lena swallows a worm that she's using like a cocktail olive. Except that the worm pleads for mercy as she drinks and then lets out a dying scream when she swallows it. It's not made any better when you realize it's a Shout-Out to The Fly (1958).
The city itself is pretty terrifying, especially for anyone expecting the bright, cheery Mushroom Kingdom of the games. It's dark, fungus-infected (and the fungus is sentient, albeit helpful), and full off strange devices and hostile people. It also has more than a few things in common with a police state, given how Toad is arrested for singing an anti-Koopa song and prisoners are hung from the ceiling in cages. Oh, and at least one form of punishment is for prisoners to be de-evolved into hulking monsters to work for the very people who did this all to them.
where a technician gets devolved into primordial slime and sloshes out of the chair and onto the floor. As Koopa puts it, "it's more than just death—it's being... undone". The reason Koopa had the guy devolved: He sneezed. We get that Koopa is a germaphobe, but it kinda makes you wonder how many people he had slaughtered for even the slightest "infraction".