In an early unused version of the "Mountain of Rubble" cutscene, Fiona is voiced by a different voice actress, but she is completely silent in the final version. In addition, there's a unique music in the cutscene that was removed in the final version, and the dirt effects when Fiona falls back down were originally brown instead of grey.

If Fiona inserts a "SALTATIO" Plate-key into a Golem, it will perform a 15 second Para Para dance, called the "Secret Dance" in the game's soundtrack, after which Fiona will remark "......That got my mind off things. I feel a little better now." before completely restoring all of her stats. "Saltātiō" is a Latin noun meaning "a dance".

In the Japanese version, the menu voice is named 'Memo', instead of 'Comment'. The Japanese version also shows 4 notes on each page, instead of 2 notes.

Believing that a female lead would not be received well, Capcom added in a dog partner that could attack enemies. After this change, they further designed the gameplay around this partner mechanic.

Rather than streaming audio files, the music for Haunting Ground was generated by using the PS2's built-in sounds. This way, the composers could easily change the tempo of the music during gameplay.