The boss called the Alpha Kretin resembles the logo of the game's development team, AlphaDream.

There is an unused item that looks similar to a Life Shroom, but is named 'Dummy'. If used, Mario (or Luigi) will throw it in the air (while inside Bowser) and it will explode, healing 60 HP back to Bowser. It was most likely scrapped because of the fact only the Sea Pipe Statue and Durmite can damage Bowser from inside.

Going to Bowser's Castle Spoiler:as Mario and Luigi and going down a blue pipe in the concession stand area will lead you to an underground room. Entering the correct code in the following room will Spoiler:open a vault, and entering the vault one finds a large icy room. Hitting the button with a hammer will cause some of the ice to melt, revealing three Spoiler: Shroob enemies from the previous installment in the series, Mario and Luigi: Partners in Time.

After the battle, Starlow finds out that these creatures once invaded the Mushroom Kingdom, and that Mario and Luigi Spoiler: defeated them as babies. Starlow also finds out that Spoiler: Luigi defeated the Shroobs by crying in the past, another nod to Partners in Time . This almost assures that the Mario and Luigi in Bowser's Inside Story are Spoiler: the babies in the previous game.

Upon meeting Broque Monsieur as Mario and Luigi at his shop in Dimble Wood, he says that he has met them somewhere before but can't remember. This is probably a reference to when Bowser first got the Vacuum Block and Broque saw Mario and Luigi inside of Bowser.

Monsieur does not like that the brothers hit the ? blocks around the kingdom and decrease their "value" and refuses to sell them anything.

In Mario & Luigi: Bowser's Inside Story, there are quite a few unused rooms without anything in them, most of them used for testing. One of the rooms appears to be a pipe in Dimble Woods leading into bowser's body that can only be accessed through the use of hacking. It was probably removed because once you've found all the attack pieces there you had no need to go back. Another one of those rooms are in Dimble Woods, along with what appears to be the Tower Of Yikk on the ground. This might suggest that originally bowser was supposed to fight it in dimble woods, but it was replaced with Bowser's Castle.

There is an unused graphic of an earlier version of the water fountain from Toad Town, with a statue of Princess Peach as a mermaid.

Certain in-game enemies are only able to be fought by Mario & Luigi or Bowser. Despite this, a few Bowser-oriented enemies have unique behaviors for Mario & Luigi, which can only be seen through hacking the game:

• All of Naplock's attacks can be dodged or countered by jumping, with its snot bubble attack also missing Mario & Luigi entirely even if nothing is done.
• Dark Mechawful's punch attack can be countered with Mario & Luigi's hammers, while its countdown attack is replaced by the same star attack used by the Dark Mechawful head, which can fight Mario & Luigi in normal gameplay if Bowser inhales it. However, in a hacked Dark Mechawful fight, this attack progresses extremely slowly.
• The smoke signals at the start of Choomba's charge attack are changed from fist and shell icons to "M" and "L" ones, indicating which brothers it will charge at and in which order; the attack can also be countered by hammering.
• Dark Trashure's thrown items can be avoided or countered by jumping, similarly to its standard counterpart. However, the items move far faster than those thrown by a regular Trashure or a Dark Trashure fought by Bowser.

While most of these behaviors appear to be failsafes, Choomba is unique in that the "M" and "L" smoke signals are not present anywhere else in the game, indicating that at one point in development, Mario & Luigi would've been able to explore the Tunnel, where Choombas are fought.

Meanwhile, when hacking the game to allow Bowser to fight enemies that can only be encountered by Mario & Luigi, most of them will either crash the game, flee immediately, or display glitchy behavior. One unique case is Magifoofas, which can be inhaled by Bowser (despite the Vacuum Block not indicating this), indicating that the developers considered letting him encounter them in some form.