According to writer Paul Gardner, there was originally going to be a character named Moronic the Plumber (a parody of Sonic and Mario) that took the role of a hero to reclaim stolen treasure from their dimension. Traveller's Tales rejected the idea, and Moronic was later replaced with a cameo from Spyro the Dragon.

There are several unused animations which can be found deep within the game's files. Most of the animations are unused attacks for Crash, nearly all of which have animations and are usable by modding the game's code. They were most likely removed due to time constraints.

There was once a character planned for the game called Capu Capu who was ultimately cut. He was originally the captain of the boat that took Crash to Iceberg Laboratory. He was cut as they had left it until the last minute to add him to the game, by which point finalizing the game had already begun.

It was intended for Fake Crash to appear as a cameo, stranded with Crunch on the small isle next to N.Sanity Island, before being scrapped for technical reasons.

According to a designer Paul Gardner, the line about Cortex almost calling Nina his daughter was added as a joke to make their relationship more mysterious. It's also hinted that she could very well be his daughter, and that only the future will tell.

The development team had plans for a sequel to Twinsanity, which would have involved Crash being transported into various TV shows via a device invented by Cortex. It never went past the brainstorming phase, due to the closure of Traveller's Tales Oxford.

Some songs from this game's soundtrack are based on pieces of classical music:

• The music from the Doc Amok segment in the level Totem Hokum is based on "Flight of the Bumblebee" by Nikolai Rimsky-Korsakov.
• The music from the worm chase in the same level is based on "The Blue Danube" by Johann Strauss II.
• The music in the chase scene with Rusty Walrus is based on the first part of "The Hebrides" by Felix Mendelssohn.

A level called "Megalomaniac Mind Mania" was cut at a very early stage of development. The Psychetron would have transported Crash into Dr. Cortex's Brainovial Hyperbarium to explore Cortex's twisted mind and discover the connection Cortex has to the Evil Twins. Every enemy character was an ugly version of Dr. Cortex and would have driven around in tanks. The whole level was to be a musical number, sung by Dr. Cortex called 'Take a Walk Through My Brains'. Lyrics for the song were written, but ultimately after the level was cut, went unused.

The Oxford division of Traveller's Tales only worked on two games in its existence: Crash Twinsanity, which the studio was formed to develop, and Super Monkey Ball Adventure.

A level for Crash Twinsanity called "Gone a Bit Coco" that took place in Coco's mind was cut late in development because it was deemed glitchy and incomplete. It can be seen in early gameplay videos, and the level music was used in the credits sequences. An unused enemy from this level, the Pink Elephant, would later appear in the 2021 mobile game Crash Bandicoot: On the Run!

Every single song in the Crash Twinsanity soundtrack was composed fully a cappella, regardless of its genre or tone, with no instrumental backing, using human voices for every single instrument. The scat group behind Twinsanity's score, Spiralmouth, would return for Crash Tag Team Racing, but the tracks in Tag Team Racing had proper instrumentals with a capella vocals.

Originally, Coco's evil counterpart was going to appear in the game. However, she was removed for unknown reasons. She still remains in a deleted scene for the game.

N. Trance from Crash Bandicoot 2: N-Tranced was originally going to make an appearance in Crash Twinsanity in a cutscene in which Evil Crash eats his brain with a spoon "like an egg". The scene was scrapped because it was "a bit gross". The only trace of N.Trance left in Twinsanity is his concept art.

Before going to the 10th dimension, Dr. Cortex says "Come now, as we explore a new dimension! It should have been two new dimensions but we... ran out of time." This is a reference to the development period of 12 months, as the development team originally wanted to put another world into the game. However, due to time constraints, the world was scrapped.

What came to be of Crash Twinsanity bears little resemblance to the original design. Originally a quest-based game called "Crash Bandicoot: Evolution", the plot revolved around Crash trying his best to help the "Gaudi" alien race while causing more problems than he could solve. The Evil Twins and the Ants served as the antagonists and were traveling to different planets to steal materials to make their own planet. The game was changed due to the plot being too similar to the Ratchet and Clank series.

Coco was originally planned to appear in the game as a playable character in a cut level called "Security Insanity", but according to designer Paul Gardner, the game's producers did not want her to have the same moveset as Crash and requested her removal. Despite this, the back of the box advertises that there are four playable characters besides Crash, Dr. Cortex, and Nina.