In the underground caves of Shinra Manor, several Coffin Keys can picked up from Sahagin enemies which can open four coffins found in the area. Three coffins contain more enemies, while the fourth coffin contains an unseen sleeping man who Zack decides to not disturb. This person is Spoiler:Vincent Valentine, who at this point in the Final Fantasy VII series storyline was Spoiler:in the middle of a long, dormant sleep after undergoing genetic experiments.

Spoiler:The shoulders of the superboss Emerald Weapon from Final Fantasy VII can be seen frozen in stasis behind a large crystal from the top of a hill in the northern part of the Depths of Judgement, the first area in the game's final dungeon, the Banora Underground.

In the Japanese version, the "Minerva Statue" seen in the Banora Underground when facing Genesis strongly resembles the Virgin Mary. But in the English release, the statue was changed to reduce ties to Christianity.

The game's main antagonist, Genesis Rhapsodos, was created as a collaboration between Camui Gackt and Hideki Imaizumi, the game's producer. Gackt's original involvement with Square Enix was in singing the theme music for Dirge of Cerberus: Final Fantasy VII, "Redemption", and appearing as a minor role in that game playing Genesis. Imaizumi thought such a passing role was a waste and asked for him to have more involvement, and asked for his help in coming up with Genesis's design, describing everything from his attitude to his clothes.

In a poll where readers of Japanese magazine 'Famitsu' were asked which games made them cry, Crisis Core came in second place, just after Final Fantasy X, which took the top spot.

Angeal's hair is a remnant of an initial design for Cloud. Cloud was originally planned to have slicked back black hair in Final Fantasy VII to contrast Sephiroph's long white hair.