Executive Meddling: The original subtitle was "Triforce of the Gods," but it was deemed necessary to change this for American audiences in case any Moral Guardians threw themselves in a tizzy over the alleged references to religion and gods. Despite this, the American manual explicitly uses the term "gods" in explaining the game's backstory and Hyrule's creation myth.
Flip-Flop of God: At the time of this game's release, the back of the box said it was a prequel to the NES installments. The story told in the manual seems to reflect this, detailing the origin of Hyrule, the Triforce, and Ganon. By 1998, however, Shigeru Miyamoto seemed to have changed his mind, stating that it was a sequel, even though this makes almost no sense plot-wise and is now mostly seen as a slip of the tongue from his part. He gave another interview in 1999 that seemed to confirm the originally-intended order.
Taken a step further when Ocarina of Time was made in 1998, which created even more Continuity Snarl (how it ends on both ways when the Adult portion ends and begins with Wind Waker and the other to Majora's Mask then to Twilight Princess). It wasn't until Hyrule Historia that the game took place after the defeat of Link, resulting timeline number 3 and eventually, this game. It also did confirm it was a prequel to the NES game, just not to the series as a whole.