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

While Bumpties can only bump into Yoshi and not hurt him, if Yoshi is hurt by a different enemy or obstacle and a Bumpty is on-screen, it will run to and steal Baby Mario similarly to a Bandit. This is the only game in the Yoshi series where Bumpties are known to behave like this, and is a rare interaction since there are few instances in the game where Bumpties and obstacles are close enough to trigger it.

In a 1995 developer interview, Shigeru Miyamoto stated that the Super Star was originally going to briefly transform Baby Mario into his adult self. However, the idea was discarded after one of the developers pointed out that it would clash with the game's premise of being an origin story for the Mario brothers. Instead, Super Star Mario was redesigned to simply be Baby Mario in a yellow cape.

In 2020, sprites for Mario's adult form were uncovered as part of a massive leak of data from Nintendo's internal servers. These sprites indicate that Super Star Mario was not originally able to float in the air and that he was able to ride Yoshi to some extent (in the final game, Yoshi reverts to an egg until the Super Star wears off).

The game was originally intended to be the fifth installment of the Super Mario Bros. series, with two leaked prototypes from December 1994 featuring a title screen with the logo Super Mario Bros. 5: Yoshi's Island. Come the final release, and the prefix would be shortened to Super Mario. This explains why the international release was titled Super Mario World 2: Yoshi's Island, as the original Super Mario World was subtitled Super Mario Bros. 4 in Japan.

Additionally, the later of the two prototypes features a radically different design for the logo, using a much sleeker and blockier font. The final release would revert to the earlier logo, barring the aforementioned truncated prefix.

The German version of the level "Touch Fuzzy, Get Dizzy" is titled "Lustiges Sporen Drama". This abbreviates to "LSD", referencing the psychedelic, disorienting effects of touching the Fuzzies that serve as the level's English namesake.

In May 1995, an interview with series creator Shigeru Miyamoto and Rare co-founder Tim Stamper about the development of Donkey Kong Country (DKC) was published in the magazine Electronic Games, conducted by game journalist Steven L. Kent. Kent later claimed on an episode of G4's docuseries "Icons" that Miyamoto was angry during this interview, channelling it into bitter criticisms of DKC's gameplay and the Western market's praise of its pre-rendered graphics, and that Stamper "sat there and took it, even though really the anger wasn't meant to be at Stamper". Miyamoto clarified in a 2010 interview with IGN that he did like the game despite these rumored criticisms, and that he worked closely with Rare and Stamper during development.

Years after the interview's publication, Kent would print an alleged portion of a later interview with Miyamoto in his 2001 book "The Ultimate History of Video Games", claiming that the anger had stemmed from "touchy" internal discussions regarding Super Mario World 2: Yoshi's Island. The hand-drawn crayon art style of that game was said to be a result of the alleged anger over DKC's graphics causing him to rebel against Nintendo's internal evaluation committee, who wanted Yoshi's Island to use pre-rendered graphics. Part of the Miyamoto quote reads:


Yoshi's Island director Takashi Tezuka would deliver a less angered statement that may be related to these claims in a September 1995 interview with the magazine Dengeki Super Famicom. He claimed that the choice in art style was done for sentimental reasons, as the developers believed that all video games from that point on would likely utilize 3D graphics, and wanted Yoshi's Island to be a bow-out for 2D graphics:

Among files uncovered in the Gigaleak, a large-scale leak of assets from Nintendo's internal servers in 2020, are various assets from Super Mario World 2: Yoshi's Island depicting alternate ideas for Baby Mario. The earliest of these assets are a series of sprites from October 1993 depicting him in a bonnet and with a mustache similar to his adult counterpart; by comparison, the earliest sprites depicting his final design are dated to August 1994.

In the interim, however, Nintendo apparently considered omitting Baby Mario entirely; sprites dating to the spring of 1994 show that the developers considered having the Yoshi Clan ferry an infant wizard around instead. These sprites depict the wizard both in normal gameplay and in the pre-rendered CGI graphics used in the opening cutscene. Other sprites of the wizard show that they would've provided an in-universe reason for Yoshi's ability to transform into various vehicles: the wizard would cast a spell on a Yoshi egg while encasing themself and the real Yoshi in a bubble.

While the developers ultimately went back to using Baby Mario, the wizard still appears in a prototype build from December 6, 1994. In this iteration, the wizard is a form that Baby Mario can turn into through the use of an item depicting the projectiles fired by Kamek in the penultimate area of "6-8: King Bowser's Castle". This "Wizard Mario" form could similarly cast spells that transform certain enemies into objects such as eggs, watermelons, and Winged Clouds.