A major bug in The Witch and the Hundred Knight that can occur at seemingly any time will force the game to return to the system menu, losing all unsaved progress as a result. This became a common critique in the game's reviews, leading it to not be received as favorably by some. While The Witch and the Hundred Knight: Revival Edition did not fully fix this glitch, it occurs much less frequently, with playing for extended periods of time being noted as a possible factor.

Originally, Nippon Ichi Software considered making The Witch and the Hundred Knight an open-world game, but this was ultimately scrapped in favor of focusing on the game's 3D graphics technology.