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In Konquest Mode, remaining idle on dialogue screens at certain points will cause a monk towards the bottom of the screen to break the fourth wall; turning around to look at the player and shrugging before resuming his original position.

In the Misty Stream area of the game, the player can find a wreckage of a pirate ship which appears to be the Phantom Storm boss from Kingdom Hearts 2, as can be seen by the identical jaw piece.

In the Arcade version's Attract Mode, Rain can be seen fighting Shao Khan for about a second. Rain was not a playable character in this version but was added to stir up rumors of his alleged inclusion.

Upon closer inspection it can be noted that Rain's name within his health bar is copy-pasted in a different font than what is standard for character names during matches.

The Insane Cults offense player Vitas Varnas is a reference to the real-life actor, producer and writer of the same name.

In the fifth mission of the bonus mode Half-Life: Decay in the PlayStation 2 port of Half-Life, the corpse of a guard can be found floating in a pool. The corpse has over 3,000 health and if hit enough times, it will destroy and spawn Snarks which can be acquired for use.

In February 2019, the game was removed from sale on Steam by the developer. This was because the game received a negative review bombing by Chinese gamers due to it featuring a poster with derogatory remarks about Xi Jinping, the president of China. Red Candle Games stated that they'd do another review of the game to make sure no other "unintended materials" were present. Additionally, all official trailers had been either made private or removed.

The studio's other game Detention had also been bombarded with negative reviews due to the outrage.

In Chapter V: Cut and Run, there is a certain breakable wall that the player can break via Jazz's Grapple ability which leads to a hallway with a switch at the end. If the player attempts to activate said switch it will transform into a robot and proceed to dance. Afterwards, a door behind it will explode revealing a hidden room.

Rumble and Laserbeak can be found as hidden cameos in chapter two and if they are shot at they will retreat. Additionally Soundwave can be found the same way but disguised as a cybertronian light fixture and he will transform, taunt Optimus, and then retreat if the player focuses their aim on him.

The autotuned part of Escape from the City Act 1 is the same melody from Sonic the Hedgehog 3's Endless Mine level. In addition, Act 2’s theme contains elements of It Doesn’t Matter from Sonic Adventure 2.

In the Egyptian-themed levels, there are hieroglyphs of black dogs on the wall that are speculated to represent Morgan T. Dog (now deceased), a pet mascot of Naughty Dog. N. Sane Trilogy kept this reference intact.

On the eastern side of the map, between Boston Common and Back Bay District, there is a door to an underground bar known as the Prost Bar. Prost, translated from German, means "cheers" and the area is a reference to the TV sitcom "Cheers" which ran from the early 80's to the early 90's.

The character Jam Kuehnemund's name is a possible reference to Jan Kuehnemund, the former lead guitarist of the rock band Vixen.

A lot of Team Rose's levels end at a much earlier point than Team Sonic and Dark's. However, through the use of glitches, exploits, or cheats, it's possible to go past the goal ring with Team Rose and go to areas that are only accessible to the two other aforementioned teams. The same thing can also be done in some of Team Chaotix's levels as well.

Interestingly, the characters of both Team Rose and Chaotix have fully voiced and functioning dialogue for these normally inaccessible areas.

In the Mojave Desert stage, the second set of oil pumps on the side of the road obscure a billboard and is usually unreadable during a race. Stopping and reading the billboard will reveal the text:

"Sometimes, God takes MOMMIES
and PUPPIES away...
And sometimes...
Just sometimes...

I do"

The Hasta La Vista Station title, tagline and mission text are all references to the Terminator franchise: The title is a phrase from the original 1984 film, the tagline "I know now why you ink..." is a reference to the line "I know now why you cry" from the 1991 sequel, the use of the word "terminate" for the mission description is unique to this mission (normally it is "defeat").

In the Octo Expansion, Stations Maverick, Goose, and Iceman are named after the nicknames of the characters from the film Top Gun. The taglines for these stations "Revvin' up your Inkjet...," "Listen to its howlin' roar...," and "Jet into the danger zone..." are references to the song "Danger Zone" by Kenny Loggins, which was used in the film.

In the Octo Expansion, the many titles and taglines of stations contain references to music from the 80s-90s:
• Roll Out Station - "Rollout" by Ludacris.
• Fake Plastic Station - "Fake Plastic Trees" by Radiohead.
• Bounce with Me Station - "Can I Get A..." by Jay-Z.
• "Just go ahead now..." Spin Docto Station - "Two Princes" by Spin Doctors.
• "Just cruisin'..." Rad Ride Station - "Just Cruisin'" by Will Smith.
• "Blowin' up like it's all good." Notorious Station - "Juicy" by The Notorious B.I.G.
• "Bring da ruckus!" Phat Splatz Station - DJ Phat Beatz and "Bring da Ruckus" by the Wu-Tang Clan.
• " Step it up!" Breakdance Station - "Step It Up" by Stereo MC.
• "As 50 yellow balloons go by..." Pop Rock Station - "99 Red Balloons" by Nena.
• "Ya like to..." Move It Move It Station - "I Like to Move It" by the Outhere Brothers.
• "Stamp-collaborate and glisten!" Stamped-Up Station - "Ice Ice Baby" by Vanilla Ice.
• "Don't just stand there..." Bust 'n' Move Station - "Bust a Move" by Young MC
• "Round round round round..." Right Round Station - "You Spin Me Round (Like a Record)" by Dead or Alive.
• "Splat magic splat!" Labyrinth Station - "Magic Dance" by David Bowie.
• "Watch out now!" Ink & Watch Station - "Watch Out Now" by The Beatnuts.
• "Gettin' dizzy with it..." Don't Ralph Station - "Gettin' Jiggy wit It" by Will Smith.
• Swass 8-Ball Station - Sir Mix-a-Lot album, Swass.
• "Inkulators, mount up!" Squee-G Funk Station - "Regulate" by Warren G and his record label "G-Funk"
• "Take it easy..." Slow Ride Station - "Slow Ride" by Foghat.
• "Don't stop 'til you pop enough!" Pop Star Station - "Don't Stop 'Til You Get Enough" by Michael Jackson, who was known as "The King of Pop."
• "Who let the pods out?" Duh-Oh Station - "Who Let the Dogs Out?" by Baha Men.
• "Might as well..." Jump Station - "Jump" by Van Halen.
• "What's the dealio?" Cubular Station - "What the Dealio" by Missy Elliot.
• "Y'all bready for this?" Toastmaster Station - "Get Ready For This" by 2 Unlimited
• Ride with Me Station - "Ride wit Me" by Nelly.
• "Ink it real good!" Ink It Station - "Push It" by Salt-N-Pepa.
• "My my my my..." Can't Touch This Station - "U Can't Touch This" by MC Hammer.
• "Can't c me..." All Eyez Station - "Can't C Me" by Tupac Shakur from his album All Eyez on Me.
• "Ink-a-zig-ah..." Girl Power Station - "Wannabe" by the Spice Girls.
• "Do not miss your chance..." One-Shot Station - "Lose Yourself" by Eminem.
• "Watch your step!" Footloose Station - "Gettin' Jiggy wit It" by Will Smith.

By playing as Peachette in the final level of Peach's Castle, the real Peach will act confused before the fight plays as normal.

One of the title's mini-games is called "Dodge Fuzzy, Get Dizzy," a reference to the title of level 1-7 "Touch Fuzzy, Get Dizzy" in Super Mario World 2: Yoshi's Island.

The names of the post-game master trainers appear to be references to other outside media:
•The Pikachu master trainer Lass Iuke is a reference to voice actress Ikue Otani who voices Pikachu in the Pokemon anime.
•The Eevee master trainer Lass Aoi is a reference to Aoi Yūki, the voice actress for Eevee in the game.
•The master trainers for Zubat and Golbat, Scientist West and Scientist Keaton, are references to actors Adam West and Michael Keaton, respectively, who both played the superhero Batman.
•The master bird trainers Bird Keeper Barney, Bird Keeper Seymour, and Bird Keeper Moe, are possible references to the characters Seymour Skinner, Barney Gumble and Moe Szyslak from the animated series The Simpsons.
•The three ghost master trainers: Psychic Arin, Psychic Danny and Psychic Ross, are references to the members of the video game web series Game Grumps; Arin Hanson, Danny Avidan and Ross O'Donovan.