The layout of the Candy level was changed in the Japanese release.

The game's story intro theme sounds very similar to the spindle scene from Disney's 1959 film adaptation of "Sleeping Beauty", where Princess Aurora was possessed by Maleficent's magic spell.

Depending on if you choose between Mickey, Donald, or both through 2-player co-op, the second section of each stage will be different. For example, in Stage 1, if you choose Mickey or Donald, the second section will be themed around giant flowers and beanstalks with a slightly different map design between the Mickey and Donald playthroughs, but if you choose co-op, you will instead be taken to an underground stage set in a mine.

In Japan, QuackShot Starring Donald Duck was closely associated with branding used for Castle of Illusion Starring Mickey Mouse, as both games were developed and released by Sega one year apart from each other. Although the title screens for both games in the Japanese versions used their international titles, QuackShot was referred to as アイラブドナルドダック, or I Love Donald Duck, in various Japanese promotional materials, while the Japanese title for Castle of Illusion was アイラブミッキーマウス, or I Love Mickey Mouse. Following this trend, World of Illusion Starring Mickey Mouse and Donald Duck was released in Japan with the title アイラブ ミッキー＆ドナ, or I Love Mickey & Donald.

Both Castle of Illusion and QuackShot would be bundled together and re-released in two different compilations in the 1990s: one for the Genesis released internationally, and another for the Sega Saturn released as part of the Sega Ages series exclusively in Japan, which used the I Love branding.