Due to a programming error, the player has a random chance of accessing debug mode in Super Mario Bros. 3 (specifically the one from the NES version of the game, which is carried over to the Super Mario All-Stars port). The debug mode only activates if a value of 80 is stored at the RAM address 7E0160, which can be manually edited by a devkit.

The NES version initializes the equivalent RAM address to 00 whenever the game is turned on, preventing the player from encountering debug mode during the normal course of play. However, due to an oversight, this does not occur in the SNES version, resulting in Super Mario All-Stars reading whatever value is generated by the console itself. Because this value is randomized during bootup, this means that the game has a small chance of activating debug mode in Super Mario Bros. 3 on a retail unit. While the theoretical probability of this occurring is 1/256, it can vary depending on the console's build and the power grid that it is connected to.

Right before the "lights" come on and illuminate the title screen, the crowd of Mario characters can be heard talking. Even though you can't really make out any words, the crowd chatter sound clip was changed for the U.S. version.

There are a few mistakes in the end credits. Birdo and Ostro had each others name, Hoopster was misspelled Hoopstar and Clawgrip is known as Clawglip. These mistakes were not fixed in the Super Mario All Stars version, but were fixed in Super Mario Advance.

There's an unused fanfare for Super Mario Bros. 2, not included in the NES version. It was eventually used as the Spade/Heart/Club House victory jingle in Super Mario Advance 4: Super Mario Bros. 3.

In the NES and SNES releases, the power-up "Kuribo's Shoe" is actually the Japanese name for the power-up, but it was left unchanged for their English releases. Kuribo is the Japanese name for Goomba, and this would later be corrected in the GBA release by naming it "Goomba's Shoe".

In the SNES and GBA remakes of the game (Super Mario All-Stars and Super Mario Advance 4), the creatures the Mushroom kings were transformed into were changed from regular animals, such as a dog or a spider, to creatures specific to the Mario series that don't otherwise appear within Super Mario Bros. 3.

If a Muncher is hit with Raccoon Mario's tail attack, it will turn into a block. This trick carried over to the Super Mario All-Stars version, but not the GBA version, Super Mario Advance 4: Super Mario Bros. 3.

The Wart boss fight was originally going to sport tomato projectiles as seen in its original incarnation in Super Mario Bros. 2. They were replaced with cabbages in the final release, but the tomato sprite is still present in the game, albeit unused.

Super Mario All-Stars Limited Edition has the smallest filesize of any Wii disc released to retail.

The NES and SNES versions of Super Mario Bros. 2 contain different insta-kill cheat codes, likely used by the game's developers for debug purposes. The code for the NES version involves pausing the game and holding Up/A/B on a second controller, and then unpausing to lose a life. The code for the SNES version is simpler, where you only need to pause the game, hold L and R, and then press Select to lose a life.

There are a pair of glitches that can be triggered with this code in the NES version. If the code is inputted while riding a Rocket, the health bar will effectively turn invisible by displaying all the heart pips as empty, but the player character will emerge unharmed. If the code is inputted during the transition for walking through a door, the player character will continually fall through the floor and lose their lives until a Game Over is reached.