In the Nocturne Mainax version that features Dante from the Devil May Cry series as a guest character, jumping from the Mantra Headquarters will normally cause your party's HP to be reduced to 1 HP. However, if Dante is in your party, he will take no damage from the fall.

In the Nocturne Chronicle version only released in Japan featuring Raidou from the Shin Megami Tensei: Devil Summoner games replacing Dante, he also takes no damage if you jump from the building.

These appear to be references to how each character can fall from great heights and land without any visible damage, such as in the beginning of Devil May Cry 2 where Dante successfully lands a jump from a tall cathedral tower.

Within the game's files is the main title theme to the Star Wars series, presumably having been used to test how the Sony ADPCM audio compression would affect the game's music.

In Shin Megami Tensei: Nocturne's "Vortex" prototype, character models for Maya Amano (from Persona 2: Eternal Punishment), Lisa Silverman (from Persona 2: Innocent Sin), Sid Davis (Devil Summoner), and Lucifer's design from Shin Megami Tensei II are present. In the final product, the first three characters are absent and Lucifer appears in two different designs.

Additionally, Lilith seems to have had an important role in the prototype, opening up a path for the protagonist. In the final cut, this doesn't happen and she is merely a normal enemy demon.

The first Magatama you get in the game has a hidden skill in it. Called "pierce", this passive skill lets your physical attacks be 100% effective on all enemies. You can only unlock this by completing the Labyrinth of Amala.

If you keep the first demon you receive, a Pixie or one of her evolved forms (High Pixie or Queen Mab), throughout the game and get her to a special door on the Fifth Kapla in the optional dungeon Labyrinth of Amala, she will evolve in to a Super Pixie.

There are three versions of Nocturne in Japan.
• The original version, which was only released in Japan.
• The second version called Nocturne Maniax, which is the same as the one released in the United States, updated with the optional Labyrinth of Amala dungeon, true demon ending and Dante from the Devil May Cry series.
• The third one, which again was only released in Japan in 2008 called Nocturne Maniax Chronicle Edition. This version removed Dante and replaced him with Raidou Kuzunoha from the Shin Megami Tensei: Devil Summoner series in his place. Raiduo, who is silent speaks through his cat, Gouto.