When Link first meets Marin in Link's Awakening, he mistakes her for Zelda. Zelda's sprite in this game is an edited version of Marin's.
In the intro for Oracle of Seasons, it's clearly bright daylight, while the intro for Oracle of Ages, it has more of a twilight-ish feel to it (observe). In the official timeline, Ages comes after Seasons, the intros to both games having hinted at that.
Between the seasick pirates of Seasons, the raft disaster in Ages, and the shipwreck surrounding Awakening, this Link clearly has terrible luck with sailing.
In "Seasons," the Maku Tree is unable to see the location of the final Essence of Nature in his dreams. That's because it's not in Holodrum—it's in Subrosia.
Twinrova being alive may seem like a plothole considering they died in Ocarina of Time, but as seen at the end of Link to the Past the full Triforce can revive the dead, who's to say that Ganon didn't bring Twinrova back after getting the full Triforce? Also a bit of heartwarming if it is true since Twinrova is the one person Ganon does care about enough to bring back with his godly power.
Many fans have noted about the core differences between the Oracle games: Seasons is more combat-oriented, challenging your ability to hold your own in combat with the sword against hard-hitting and fast enemies. Ages is more puzzle-oriented, challenging your ability to use your items in unique, and ever-complex ways. Now, what are the names of the oracles in either game? Din in Seasons, who shares her name with the Goddess of Power, and Nayru in Ages, who shares her name with the Goddess of Wisdom. Going back to the key differences of both games, it's clear that both represent two parts of the Triforce: Seasons is intended to test your Power in combat and Ages is intended to test your Wisdom in puzzle-solving.
The Oracles series was originally going to have three entries named after the three pieces of the Triforce. CAPCOM initially intended for the three games to be played and linked together in any order the player chose. Due to the difficulties in linking the three games via passwords, they decided to make the three games into two games. The game titled for the Triforce of Power became Oracle of Seasons, the game titled for the Triforce of Wisdom became Oracle of Ages, and the game titled for the Trifoce of Courage was essentially scrapped. Instead, Farore cameos in both games.