- Neglecting to retrieve Baby Mario in time rewards you with an image that consists of the Toadies carrying Baby Mario away against a black background, with one of them snickering at you before they take off. The noise they make doesn't help.
- The "Game Over" screen shows "GAME OVER" in a deranged font zooming in and rotating in random directions. The same animation repeats itself several times afterward until you either continue the game or shut it off. The depressing piano ditty that plays under it and the fact that SNES games with pre-rendered 3D graphics were in their relative infancy only make this worse.
- Fuzzies from "Touch Fuzzy, Get Dizzy" trigger an extremely jarring Mushroom Samba when touched, and the way they float around in groups and take up so much space makes avoiding them a nightmare. The fact that they mess with your egg throwing and movement doesn't help matters.
- Lunge Fish: giant catfish that try to swoop up from the water and swallow Yoshi whole for an instant death.
- The sub-boss of world 3, Prince Froggy. Up to this point Kamek has made all the bosses bigger... In this case, he makes Yoshi small and is promptly eaten by Prince Froggy. Yoshi's sheer horror after he... "exits" Prince Froggy speaks for itself.
- World 6. The first five worlds in the game all have some sort of charming quality to them for the most part: Smiling flowers, adorable-looking fauna and lush-looking backgrounds. Then you find yourself in the hellish wasteland that is World 6. The ground is brown and dead, all the forest's trees have been petrified, bones and Skeleton Goonies litter the landscape and lava flows freely in nearly every level.
- There is an optional chase in the final level where Tap-Tap the Golden, an invincible golden version of Tap-Tap the Red Nose, is chasing Yoshi across a rocky, lava-filled area, as the screen ever so slowly autoscrolls to allow him more area to move. It doesn't help that before entering this chase, if the player wants to receive helpful information, all they get is "RUN AWAY, HURRY!!!" in dramatically huge font, as shown in the image above. What arguably makes this even worse is that you're being chased by a boss that's Nigh-Invulnerable, and is large enough that you can hear the ground quaking from every step that it takes. Your eggs manage to stun it, but that's about it. Not even it falling down a hole to its doom can stop it; it just springs forth like a proverbial bat out of Hell, and continues to chase you, its smile almost taunting you. Also, in the SNES version, the boss theme plays during this chase. But in the GBA version, the music that plays is when you're about to encounter a boss, which just makes it worse.
- In the final battle, where Baby Bowser, in an eerily designed toy room, attempts to ride (and therefore injure) Yoshi. After he has been defeated, Kamek turns him into Big Bowser. Big, meaning the castle he had occupied is completely destroyed by his transformation, and he could probably crush Yoshi with a single finger/claw. The transformation and battle is accompanied by hardcore heavy metal music, a jarring contrast to the other music in the game, and the battle is pretty much Yoshi trying to hit him with large eggs to push him back, while he is slowly coming towards you. When he is hit, he is indeed pushed back, only to then run at full speed towards Yoshi, who is standing on a small ledge (which is being destroyed by the boulders that fly in the air from Bowser's roars). If Bowser comes close enough, his stomach obliterates the ledge, leaving Yoshi unable to do anything but plummet to his death. This can be extremely scary when one is desperately trying to get him further back, knowing that he will run at full speed afterwards. What makes this even worse is that when he has one hit left, he'll continue to run towards you, and will not stop until he collides with Baby Mario and Yoshi. And when he does... His design◊, especially the Glowing Eyes of Doom, certainly doesn't help matters.
- "The Impossible? Maze" is one of the extra levels in Yoshi's Island, and is quite possibly one of the eeriest levels in the game. As the name suggests, it's a dark labyrinth that is seemingly endless until you know exactly what to do. It's also one of the very few levels to feature Grim Leechers, which are purple ghost-like enemies that latch onto you and reverse your controls. If that's not bad enough, the soundtrack that plays in this level in the "Room Before Boss" theme.
Nightmare Fuel / Yoshi's Island