When speaking to the Floodgate Keeper after opening the floodgates of Spool's Swamp in Oracle of Seasons, a glitch occurs where he will say the first two lines of Impa's dialog.

When you play any of the two Oracle games on a Game Boy Advance there will a special shop in Lynna Village called the Advance Shop or 100 Rupee Advance Shop. All the items on sale cost 100 rupees: a Gasha Seed, a Magic Ring and an Advance Ring. In Ages, it's adjacent to the Shooting Gallery and in Seasons to the Know-It-All Birds Hut. However, it's not available in the 3DS Virtual Console version since it runs on the Game Boy emulator. The shop is run by Stockwell, who is amazed you found the place.

According to the Hyrule Historia, there was originally supposed to an item called the Magic Paintbrush in the game. Concept art for Nayru shows her with this item. It was created to make use of the Game Boy Color.

Depending on which animal Link befriends, the landscape of certain areas in Holodrum and Labrynna will change. If Link had Moosh join them, some areas within these regions will resemble a wasteland-like area filled with many pits that Moosh can fly over. If Link had Ricky join him, then some areas within these regions may resemble a prairie-like landscape with the occasional cliffs and a couple of holes that Ricky can jump over. If Link had Dimitri join him, then some areas within these regions may resemble a large lake or river with many waterfalls, which will require the use of Dimitri's help.

The first dungeon in Oracle of Seasons is reminiscent of the Eagle Labyrinth from the original The Legend of Zelda. The layouts are similar and the exterior of both dungeons are dead trees.

In the NTSC (USA) release, Holly mistakes Link for Santa Claus, whereas in the PAL (European) release, she mistakes him for a chimney sweep.

Early concept art of Onox found in the Hyrule Historia shows him having a battle axe attached to his ball and chain.

Early concept art of Ganondorf seen in the Hyrule Historia show a design of him being more humanoid.

The Goron Vase in Oracle of Ages is an anomaly in time. It's given to Link by the Goron guard in the present after Link gives him the Rock Brisket. Link then gives the vase to the Goron guard's ancestor in the past, in exchange for a Goronade, for it to become a Family heirloom, which appears to create a paradox.

Onox's name is misspelled twice in Oracle of Ages as 'Knox'. The first time is when Twinrova announces that the three flames are now lit, saying that the Flames of Sorrow and Destruction were lit by "Veran and Knox". Later when battling Twinrova, she announces that she will "not fall like Knox or Veran". Curiously, this does not occur in Oracle of Seasons.

If all Ns are entered in the secrets section when making a profile in both Ages and Seasons, the resulting file will be a standard linked adventure but with glitched names for Link and the child of Bipin and Blossom.

There was a third game in the works titled "The Legend of Zelda: Mystical Seed of Courage." The name comes from the original titles of Oracle of Seasons (Mystical Seed of Power) and Oracle of Ages (Mystical Seed of Wisdom). The game was meant to come out several months after its prequels to form a trilogy (like the triforce), but was scrapped after complications arose with linking the three games together.

Although the commercials for both games show an Adult Link as the main hero, the boxart and game itself uses a Link closer to Young Link instead.

Oracle of Ages and Oracle of Seasons are the only games in the series that truly intertwine, allowing the player to receive bonuses and upgrades in one game for linking it to the other. Linking the games is also the only way to truly finish the story as the final bosses only appear at the end of a linked adventure.