In North America, Harvest Moon 64 is rated E for Everyone by the Entertainment Software Ratings Board despite the game's content warning stating that it contains "Use of Alcohol and Tobacco". While Nintendo of America was known for its strict censorship policies in the 1990's, all known instances of alcohol and tobacco use in the game were left intact for the North American release. The presence of tobacco in the game is very minor, with one known instance being in the overworld sprites of the Head Carpenter as he can sometimes be seen smoking a long pipe. On the other hand, wine, liquor, beer, and the social bonding aspects of drinking culture have a larger presence in the gameplay and the world-building of Flowerbud Village, including a side quest to restore the Moon Mountain Vineyard.

There is an unused character with unfinished dialogue in the game's files that likely would have been a potential marriage candidate: Princess Vanilla from the mythical Prune Kingdom. Her general storyline prior to the unused event "Princess Vanilla and the Turtle" features her getting kidnapped by a mole, being cursed to take the form of a turtle, and was going to be forced to marry a frog in this form. The player finds the princess after she had been talking to the Harvest Sprites. She explains in the event that she has not been seen in a long time by humans, but all the bachelorettes seem to have the ability to see her. If he chooses to pick her up, despite her warnings that her curse is transferable by touch, he will become a turtle as well. After this, the player learns from her that the only person that can reverse the curse is a friend, and he proceeds to wander around and talk to the villagers so they can react to him. Eventually, upon interacting with the bachelorette the player has the highest affection with, he returns to normal, and proceeds to turn the princess back into a human as well. From then on, Princess Vanilla stays in Flowerbud as a regular character and seems to have the same amount of events that the other marriage candidates have as your relationship progresses, including special scenes with all five bachelorettes and a line about having a child with the player.

On the title screen, Natsume is spelled "Natume".

Due to an error in the game's code, it is possible to get the full heart meter on Karen on the first day by simply going to Duke's bar at the end of the first day and showing Karen the player's dog over and over again. Her heart meter will continue to fill and will unlock all heart events.