In stage "Extra 3: More Monkey Madness", a 21st Red Coin can be found. The coin is hidden under a peg occupied by a gray Tap-Tap, with a rotating Paddle-Wheel above it, making it difficult to access. In the Game Boy Advance port, this coin is removed, indicating that it may have been present in the SNES version due to either a glitch or mistake.

Among the assets present in the Gigaleak, a large-scale leak of internal server data from Nintendo in 2020, are sprites for what appears to be an early version of Hookbill the Koopa with a radically different design. This iteration bears a strong resemblance to Birdo, though with numerous Koopa-like elements (including the shell, body type, and gait) that would be retained in the final game. This early design appears to explain why Hookbill the Koopa regurgitates eggs when Yoshi stomps on his head, given that spitting eggs is one of Birdo's staple abilities in the Mario series. Furthering this, some of the early sprites include ones for spitting spiked balls as an attack.

During the second phase of the final boss fight in the SNES release, Baby Bowser has three fingers on each hand, contrasting with most official portrayals of Bowser, which show him with four. This error is fixed in the Game Boy Advance version, which redraws his sprites to give him the proper number of fingers.

Early designs of the Toadies in the ys_romX_0 prototype of the game show that they originally resembled Snifits.

Leaked development files for Yoshi's Island show graphics of a razor blade hazard or weapon, possibly intended to be thrown by an enemy. This was likely removed from the game over concerns of violence and/or imitability.

According to Plok co-creator Ste Pickford, Mario creator Shigeru Miyamoto considered an early build of Plok to be the third best platforming game behind his own Mario in first, and the rivaling Sonic The Hedgehog in second. He reportedly expressed interest in helping Software Creations make Plok of a higher quality than Sonic, even if not Mario. Ultimately, he passed up the opportunity, with Pickford believing it was due to similarities with the then-unannounced Super Mario World 2: Yoshi's Island.

In a 1995 interview with Shigeru Miyamoto published in the September issue of Haou magazine, he was asked about how long it took to develop the game? He responded:

The North American commercial for the SNES version featured a man at a restaurant eating enough food to literally explode. This is a reference to the Mr. Creosote sketch from the 1983 movie "Monty Python's The Meaning of Life."

It's possible that Tweeters were originally going to appear in the game. Tweeter graphics from Super Mario All-Stars appear in the game's code, and could have been placeholder graphics for the enemy.

The enemy "Harry Hedgehog", a fast moving blue hedgehog, is thought to be a subtle reference to Sonic The Hedgehog.

In the German version of Yoshi's Island, Naval Piranha is named "Audrey", referencing the 1960 film "The Little Shop of Horrors".

In "World 6 - Extra" in the Japanese release, Yoshi's name is spelled out as "Yossy" during the segment in which the player must jump on a number of moving platforms. This was changed in the International version to spell out "Yoshi".

In the game's ROM, empty levels slots are filled with copies of World 1-1. These slots can be accessed through the use of hacking tools. When one of these levels is accessed in the Japanese version, a special title card will be shown which translates to "Yoshi's Island - Hollow Grassland".

Inside the game's data is an unused and alternate sprite for Yoshi spitting watermelon seeds. The sprite is not as puffed up as the sprite in the final version.

In the Game Boy Advance version of the game, dying enough times during the intro level to get a game over will result in the game's save file displaying "World 0." This is the only time this icon is accessible in the game, and in any version of the game, as the Super Nintendo original gave you infinite lives to beat the tutorial level.

If the game detects anything other than a control pad plugged into either port, an error message will pop up until the offending controller is removed. The color of the text changes every frame, gradually cycling through the entire 32,768-color palette.

The enemy "Burt the Bashful" looks like Obelix from "Asterix". This was referenced in other language versions of the game. The boss's name in the French version of the game is 'Belixo', an anagram of Obelix. In the German version of the game the boss's name is Xilebo, Obelix spelled backwards.

There are several unused enemies and enemy behaviors. The unused enemies include a Red Bullet Bill and Cannon, a double swap platform and a Bloo Blah holding a Piro Dangle. The unused enemy behaviors are Egg Plants spitting bubbles at a regular interval and three Cactus Jacks falling down and forming a stack.

When approaching the boss Naval Piranha, the player can see him in his un-transformed state and can fire an egg at him. Doing so results in him dying instantly, and Kamek flying in to yell "OH, MY!!!" before flying away in retreat.

An unused monkey enemy can be found in the game's graphics. They look to be similar to Donkey Kong in the style of Yoshi's Island, including a barrel that would have presumably been thrown.