If you have a full inventory up until the point where Porky's mom squashes Buzz Buzz, he will notice that Ness can't hold the Sound Stone right now and won't give it to him. Instead, he will transport it to Tracy, meaning that you don't have to hold the Sound Stone in your inventory for the entire game and it will still record the melodies of the "Your Sanctuary" locations even in Tracy's possession. Normally, the Sound Stone remains in your inventory for the whole game and cannot be held by Escargo Express. If you do wish to have the Sound Stone back from Tracy, you must talk to her in-person.

As revealed in development files uncovered by the Video Game History Foundation, the woman in Summers who sells Magic Cakes was originally intended to be a masseuse whose oil massages could induce relaxing dreams. This would've more readily explained why Ness and company's first use of her services results in the odd transition into Poo's training in Dalaam, in which the screen turns pinkish-purple and distorts before fading to black.

In a 1997 interview with the game's composer Keiichi Suzuki published in the GSLA, he stated that him and his team did an about-face in their approach to composing the soundtrack, from attempting to create vocal-oriented pop music like in Mother, to concentrate on making solid instrumentals:

The music that plays in Onett's Arcade contains brief snippets of the main theme of Xevious, and of the bonus theme from Nintendo's 1979 arcade game Sheriff.

An infamous scratch and sniff ad for EarthBound, featured in magazines around the time of the game's release, caused WayForward director/designer James Montagna to suffer from a severe allergic reaction as a child, which had him rushed to hospital:

If the player enters Threed's circus tent and repeatedly uses the Check command on the rightmost corner, the game will glitch in a variety of unpredictable ways. The most minor of these outcomes involves a short delay in when the "No problem here." text box is thrown up, while more major results can escalate into full-scale corruptions; most results involve the text box spewing garbage data. The reason for these phenomena is because of a programming oversight: the game stores every map in a single file that players are transported around via warps. However, the corner where the glitch occurs contains a gap in the room's boundaries, enabling the player to use the Check command on out-of-bounds areas that the game was not programmed to read.

Following its discovery, the bug, popularly known as the "Threed Tent Glitch" and the "Check Area Glitch," became a key asset for speedrunners, as one possible effect gives players access to a debug menu, from which they can warp directly to the game's epilogue. Its utility only further increased after players discovered that it can be triggered very early in the game by using additional glitches to reach the top-right corner in Onett's map, which similarly gives access to an out-of-bounds area.