In the Nyakuza Metro DLC, there is a hidden area that can be accessed in the Green Clean Station by jumping off of a moving subway train at the last second and then wall-jumping up to the top of a large, green, three-tiered LCD display above the station ledge. At the top, a cage with an egg can be found, but just near it is a Springboard that will send Hat Kid to a hidden, burning, grated area through a manhole. Upon interacting with the manhole, a message can be found on it that reads "Kiwami means extreme." Suddenly, an eye-patched Metro Cat named Meowjima will ambush you by jumping out of the manhole and screaming:


This initiates a secret mini-boss battle. The message on the manhole is a reference to the tagline of the game Yakuza: Kiwami, and this character is a parody of Goro Majima based on his appearance in that game as well as a reference to one of its side quests "Majima Everywhere", where he ambushes Kazuma Kiryu through disguised encounters as a form of training. There is no reward for completing this boss battle, and upon interacting with the manhole again you will be sent back to the Springboard you used to enter it.

In Hat Kid's spaceship, waiting 20 minutes will cause the music to go silent, before a loud, inexplicable groaning noise plays in the bedroom.

Jonas Kaerlev was concerned about bringing the game to Kickstarter, because he thought people would associate it with Donkey Kong 64, rather than other titles of the genre.

"It did worry us before we launched the Kickstarter. But we thought if we emphasized enough that we were trying to make something less like Donkey Kong 64 and more like Banjo-Kazooie or Mario 64, we thought it would be much more well-received."

Jonas also stated the lack of collect-a-thon platformers was partially because of Rare's Donkey Kong 64 game.

"I don't want to blame it all on Donkey Kong 64, but it's partially at fault. Donkey Kong 64 did a lot of things wrong, in that it was very tedious to collect everything in order to move on. A lot of people don't want that. They want to be able to breeze through the game if they so desire, but there are also people who want to collect everything, and get stronger and better."

In the Beta version of the game, there was a milkman NPC that was a Mafia member in a milkman suit. For some reason, the Milkman was not present in the final release of the game.

In Act 4: Train Rush of Chapter 2: Battle Of The Birds, a T.V references the intro to Kirby's Adventure.

In Queen Vanessa's Manor, there is an entire third floor that went unused in the final build of the game, along with what appears to be a shadow version of Hat Girl. The reason why the floor was cut was simply because the developers didn't like how it turned out. It is still in the game, but it cannot be accessed through normal play.

YouTuber Jon Jafari (also known as JonTron) voiced the Jazzy Penguin in the game's prototype. He was originally asked to voice a different character, but the developers thought his voice didn't match the proposed character, and instead made him the voice of the Jazzy Penguin. However, Jafari's lines as the Jazzy Penguin were scrapped at some point during development, and he instead voiced the secretary of Dead Bird Studio in the final game.

The "Peace and Tranquility" screen in Death Wish mode and the associated "Smug Dance" taunt (both added in the Seal the Deal DLC) are parodies of "No one's around to help.", a YouTube video by JerryTerry which depicts the Animal Crossing character Bob dancing to a remix of the Animal Crossing: New Leaf title theme. After the taunt was revealed in the announcement trailer for the DLC, JerryTerry responded by posting "No one's around to hat.", a recreation of the original video using the clip of Hat Kid and Bow Kid performing the taunt in the trailer. This video was uploaded only 24 days before the DLC's release, leading some players to mistakenly think that this follow-up video was what the "Peace and Tranquility" screen was referencing.

Among the costumes added in the Seal the Deal DLC is the Virtual Kid costume, which replaces Hat Kid's regular model with a low-poly version as a nod to late 1990s collect-a-thons (which the game is a throwback to). Within the game's code is an unused additional shader for this costume which mimics the distinctive jitter found in titles for the original PlayStation. Reportedly, this additional effect was disabled because director Jonas Kaerlev didn't consider it a good match for the game's "cute" aesthetic.