The Japanese and Korean releases radically alter the final boss theme, adding a second movement and raising the pitch of the French horn soundfont. This version of the music also changes the loop to start at the added portion rather than going back to the beginning of the song. The extent of these changes implies that the music was unfinished when the original international release came out.

Pre-release screenshots and the game's trailer reveal that the boss, Big Guy the Stilted, would have originally been a regular Shy Guy made huge, instead of being a robotic Shy Guy (as he is missing the patches on his sprite). Another screenshot shows that a black Yoshi was going to fight the boss at one time in development.

The logo on the side of the game's early box art shows that it was intended to have online functionality, but no such feature is present in the final game.

Although Baby Wario and Baby Bowser don't have Character Coins in the game itself, graphics for them still exist in the game's code.

The United States Environmental Protection Agency (EPA) had used music from Yoshi's Island DS for their Flash game "Recycle City". After it had been discovered in 2019, the EPA denied claims that they had stolen music from Nintendo claiming it had been made by a contractor, and that "we are looking into whether the contractor received permission to use the music, to the extent permission was necessary in this instance." Since then, the song has been removed from the game's soundtrack.

While Flashing Eggs make cameos in the Secret Level "Yoshi's Island Easter Eggs", they are out of Yoshi's reach due to them being embedded in the ceiling at the start of each room. Hacking the game to let Yoshi use them shows that they are fully coded and retain their functionality from Super Mario World 2: Yoshi's Island, producing a Red Coin when thrown at an enemy or Winged Cloud.