AnachronismThe game takes place in the 16th century, but the city known as Istanbul in the game doesn't take this name until 1930. It should be called Constantinople.
BugsA bug in the game's programming may cause half to 3/4 of your crew to suddenly vanish into thin air while you're sailing.
Version differencesDue to Nintendo of America's policies on religious imagery and usage in games, the US versions of the NES and SNES editions of the game have the "Houses of Worship" area of ports changed to "The Round Earth Society". The option there that lets the player "Pray" has also been changed to "Study", however both versions of the game allow the player to donate money towards the organization.
Information also contributed by Indra is here and WildKard