Brand new sprites of Junior can be found in the game's data, suggesting he was supposed to appear in the game.

The music 'BGM A' in both the Arcade and NES version is a more crude rendition of Nikolai Rimsy-Korsakov's 'Flight of the Bumblebee'.

The relationship between the protagonist of Greenhouse and Stanley from Donkey Kong 3 is ambiguous. The manual for Greenhouse - written before the release of Donkey Kong 3 - simply states the character to be named "The Fumigator", while print and TV commercials released after Donkey Kong 3 claim the character to be named Stanley, likely as a retcon of sorts to tie in with Donkey Kong 3.

Notably, Stanley is the only character from a Mario universe game that Mr. Game & Watch transforms into in Super Smash Bros. Ultimate, while moves based on games such as Mario's Bombs Away and Donkey Kong Junior have him retain his appearance as the pedestrian from Fire as he did in previous Super Smash Bros. games. Additionally, Super Smash Bros. Melee's trophy description for Stanley lists his debut as Donkey Kong 3 and not Greenhouse.

Ports of Donkey Kong 3 were developed by Hudson Soft for Japanese personal computers such as the NEC PC-8801 and Sharp X1 in 1984. These versions of the game were different in that Stanley is unable to jump, protecting plants is removed from the game, and most notably, the game's levels tell an ambiguous but bizarre story. The level backgrounds display a vastly different setting from the original arcade version, having Donkey Kong and Stanley traveling down a highway, encountering aliens, going to outer space, and landing on an alien planet. In the NEC PC-8801 version's manual, Hudson Soft encouraged players to develop their own explanation of the game's story and share it with them via mail.