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.

Early concepts of Dingodile had the character completely naked, with a black canine nose and being built more like an actual crocodile. Later concepts added clothes, such as dungarees, a shirt and a slouch hat.

Early designs show that Dr. N. Tropy's personal time machine was originally designed to look like a giant digital watch around his waist. Further designs changed the shape and added more gears, chronometers, pistons and exhausts. The digital clock face was eventually replaced with a traditional analogue face.

Toys for Tiny Tiger and Dingodile were created by Resaurus Toys, but were only seen at a convention. It's not known if they were from the unreleased series 3, or just scrapped figures from the previous series.

Doctor Nefarious Tropy was added to the game as the developers felt a time travelling boss was needed, as the game focused on time travel. His shortened name, N. Tropy, is a pun on entropy, a term used to measure randomness and disorder over time.

The twentieth level's name, "Tomb Wader", is play on the name of the Tomb Raider series.

At the title screen, if you press Up, Up, Down, Down, Left, Right, Left, Right and Square, a Spyro the Dragon Demo will be available to play.

Two levels in the game are named after past Naughty Dog games; Ski Crazed and Rings of Power.

The Japanese version of Crash Bandicoot 3 has five short Full Motion Video's within the game.

Once you beat the game 100%, you can find Fake Crash dancing in the levels Toad Village, Makin' Waves and Hog Ride.