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.