In the lobby of Bowser's Castle, as a hidden Easter Egg, just before Bowser fights Midbus, a Shroob can be seen in the seat on the lower right-hand corner. If Bowser tries to speak to it, it stares blankly and says "...".
The title of the game is a parody on the term "inside story", meaning the "true" tale of an event from the perspective of an insider who participated in the action, as opposed to an outsider who only hears about the event later on. In this case, the game is a literal inside story, as Mario and Luigi have to adventure through Bowser's insides.
The game's European Spanish, European French and Italian name is a parody on the famous novel A Journey to the Center of the Earth.
There is an alternate ending that happens when the player beats the game over level 40, thus getting the Final ranks for both Bowser and the Mario bros. In the ending, a voice congratulates the player.
The Mushroom Kingdom Tribune, a promotional newspaper sent by Nintendo via e-mail, includes news about the releasement of Mario & Luigi: Bowser's Inside Story.
A few typos exists in the English version's script of the game. When Bowser talks to a Wiggler in the garden in Dimble Wood after he eats the big carrot and says "Dont start, pal! We had a deal!" the apostrophe in "Don't" is missing.
Some of the Emoglobins are missing the dash when they speak (ex. "legends speak of the Biggish star panel beneath my goblin").
If one is controlling Bowser, then switches to Mario/Luigi inside him, the player will notice a remix of the song in the area Bowser's in plays.