A certain beta screenshot depicts Mario, Luigi, and their baby selves fighting two red-shoe-clad Blooper foes in the Vim Factory. The Blooper still exists in the game’s code under the name “Scoot Bloop” but it’s attacks in battle are unfinished. It has sprites for the overworld as well. Although the screenshot depicts that they were meant for the Vim Factory, it’s enemy data is grouped with the Yoshi’s Island enemies, and it’s stats make it comparable to the enemies in Yoob’s Belly.
Another early screenshot shows the gang using a Mix Flower on two Boo Guys in Hollijolli Village, while Boo Guys were not present in this area in the final game.
Finally, it may be notable that Baby Mario’s initial artwork erroneously depicted him as having red shoes rather than his normal blue ones (this mistake was eventually changed and the artwork was re-released), although his shoe coloration would appear to have always been consistent throughout all of the actual game’s programming. [Info from Mariowiki]