The United States Environmental Protection Agency (EPA) had used music from Yoshi's Island DS for their Flash game "Recycle City Challenge." 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.

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 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.

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.