The Sega Saturn version of the game contains hidden files that can only be accessed when loading the game disc on a PC. 15 pieces of character artwork and a text document containing messages from 13 of the Saturn version's developers including graphic artists, sound team members, and programmers can be found. The messages contain insights about their duties, goals and struggles in porting the game from the PlayStation to the inferior Saturn, with several members of the staff having just entered the video game industry and joined Konami prior to work starting on the port. Collectively, they had mixed to positive feelings about the final result, with most being happy with their work, while others feeling they had failed to live up to the PlayStation version. Regardless, much of the staff thanked players for playing the game and encouraged them to mail feedback to them at Konami. Two notable details from these messages include: a story/rant shared by programmer Hideto Imai in the last and longest message about his experience in violating Japan's Motor Vehicle Storage Act by parking his car curbside while staying at his in-laws during development; and a scrapped character idea shared by graphic designer Yoshinori Suzuki:

There are a large number of unused dialogue pieces in the Symphony of the Night's data, including what may be an unused ending. Many of these sound files are alternate versions of voices that are already used in the game, but extended or slightly different.

A series of clips can be found in the game's sound files, which seem to be an unfinished ending. It seems to suggest that Maria intervenes in the fight between Alucard and Richter, where she becomes possessed or transformed by Shaft. It includes both winning and losing quotes, and ends with Alucard reflecting on the apparent death of both Richter and Maria. While the PlayStation Portable and Saturn versions allows a fight with Maria, it is not under these circumstances. There are no other suggestions towards this ending, but it is assumed to be an alternate ending during the fight with Richter when not using the glasses.

The Saturn version includes a number of extra areas and features unavailable in the PlayStation version. Most infamously being that of the Underground Garden, as the entrance is still visible in the PlayStation version, though inaccessible. The player can glitch the game into allowing access to this area, but it is unfinished and only a glitched out save point is available.