I Knew It!: When it was originally released, Minish Cap was believed to be the first game in the timeline. The guidebook Hyrule Historia later reveals that Minish Cap really was the first game in the timeline when it was originally released in 2004 (albeit not for the same reasons why fans thought it to be the case) and it held the position of first game in the timeline until 2011 with the release of Skyward Sword, which was set even earlier.
New Work, Recycled Graphics: The game recycles a lot of spritework from the Four Swords games. This makes sense, as this game is a prequel to said sub-series.
Orphaned Reference: Although the Fire Rod was removed from the game and replaced with the Flame Lantern, the European version of the Ice Wizzrobe's figurine still advises you to "hit them with your Fire Rod!"