In October 2004, the men's magazine Playboy ran their first annual feature article with pin-ups of female video game characters. Among the women included was a topless render of Mileena as she appeared in Mortal Kombat: Deception, with only her sai covering her nipples. The image is also found in the Production Art gallery in Mortal Kombat: Deception under the name "Sexy Mileena", and described as "a team favorite as a desktop background and was originally created for a men's lifestyle magazine."

In the game files, some debuting characters and arenas are referred to with their internal production names:

• The Falling Cliffs stage is named "kollapsing_kliffs"
• The Nethership Interior stage is named "netherbelly"
• Havik is named "skab"
• Shujinko is named "monk"
• Monster is named "freak"
• Darrius is named "cassius"

When fighting Onaga, the game's final boss, if the player uses kicks on Onaga over and over again, Onaga will shout "No more kicking!"

In Tanya's Kombat Kard, she is seen wielding a Naginata, before it was ultimately reassigned to Hotaru. Tanya would later wield the Naginata in one of her variations in Mortal Kombat X

By performing a Fatality and a Hara-Kiri at the same time, the game will glitch out having the defeated opponent still standing in a pose like a fatality was performed on them, however the winning character will be destroyed as if they performed their own Fatality on themselves. The victory message at the end of the animation will read "-character- Wins! Hara-kiri"

In France, the name had to be changed to Mortal Kombat: Mystification. This is due to the fact that the word "déception" is French for "disappointment".

In Ermac and Sindel's endings, Kitana is shown as looking like Mileena's primary costume, but pallette-swapped with blue instead of pink. The reason Kitana has a blue version of Mileena's outfit is because she was originally going to be playable in the game, but was replaced by Jade because the creators wanted to bring back older characters.

On "The Portal" stage, off to one side are the fighting ladders from Mortal Kombat I through IV, complete with portraits.

Many of the people in the Netherrealm and the Chaosrealm sound like they're talking gibberish, but are actually speaking backwards. In fact, the actual spoken quote for each person does not match what is being said. Examples of what some of these characters are saying include (but not limited to):

"There are many realms,"

"I am talking backwards - spooky, isn't it?"

"Parents of the world, there is no satanic messages hidden within the backward speech of Mortal Kombat."

"John Vogel is a genius."

John Vogel is a Mortal Kombat developer.

Dairou was originally planned to be introduced in Mortal Kombat: Deadly Alliance but was cut due to time restraints.