In Solo Mode, the Shrinky Bean only appears in two chapters. It first appears in Chapter 6 but only if Dark Pit hides in the underground area of the ruins. It also appears in Chapter 13 at the end of the hall after Pit drops into the sandy whirlpool.
Users who eat these beans are shrunk down to a smaller, harder-to-hit size. Shrinky Beans don't affect attack power, making them doubly effective. However, being small won't protect you from wide-ranging attacks, so watch out!