When Lynx and Serge switch bodies with each other, Serge gets an updated portrait to reflect Lynx entering his body and becoming the evil boss Dark Serge. However, Lynx was originally planned to receive an updated portrait of his own when Serge enters Lynx's body and gains a more protagonistic personality, but this was scrapped in favor of Lynx's standard portrait. The miniaturized version of the unused portrait can still be seen on the equipment purchasing screen, but not in full.

When Black Hole is used while battling on the Chronopolis defense islands, one of two different images will briefly flash in the sky as the spell is being cast. The first image depicts an elderly woman in a robe, while the second image depicts a middle-aged woman and a child standing next to what appears to be a wooden art figure. These are pictures of the statues that reside on each of the defense islands; Atropos (Past), Clotho (Present), and Lachesis (Future).

Serge's default weapon, Sea Swallow, is believed to be a tribute to the NES game Ninja Gaiden, a game that Chrono Cross' producer also worked on. Irene Lew's CIA codename in Ninja Gaiden was Sea Swallow.

Spekkio is believed to make an appearance in the Bend of Time. If Janice is brought to the area, the timekeeper will note that the "God of Combat" has taken an interest in her, and she will be bestowed her level 7 tech, What'sUpDoc. He still has his own separate room, and after a trial similar to the one in Chrono Trigger (involving running three laps around the room) he offers a battle with Ozzie, Slash, and Flea. A minigame ensues in which the player must run a correct number of laps to receive a Dreamer's Sarong. After the minigame is won, he remarks that perhaps he will see the player in another, different dimension.

Sprigg is a variation of sprig, which is a leafy shoot or twig. Sprigg may also be short for Spriggan, a type of wood fairy or pixie. Since Sprigg is a Green Element and a generally woodsy being, either name would be fitting.

The player can partake in an optional fight against Slash, Ozzie, and Flea from Chrono Trigger while playing New Game Plus.

Grobyc is a cyborg, and his name is just the word "cyborg" reversed.

Masato Kato has gone on to state that Robo, from Chrono Trigger, Spoiler:is the Prometheus Circuit.

Orlha's name stems from the Irish name, Órfhlaith, which translates to "golden princess". Evidently, this fact seems to refer to Orlha's hair color.

Pierre and Harle speaks with an interlanguage called Franglais, which is a blend of English and French.

At one point, Leah says that she would name her child Spoiler:"Ayla" after going home. This could mean that she is either Ayla from Chrono Trigger's mother, or is simply referencing her.

The rock star Nikki's name is a reference to the rock star Nikki Sixx from Mötley Crüe. In Japan, the character's name is Slash as a reference to the English name of Soysau from Chrono Trigger, which is also a reference to the guitarist, Slash, from Guns N' Roses.

Chrono, Marle, and Lucca makes a cameo appearance in Opassa Beach. Using the Astral Amulet, you can talk to the original cast of Chrono Trigger.

Magus was meant to make an appearance in Chrono cross. He was scrapped because Squaresoft thought that his complex backstory would be too hard to fit into the game. He was eventually replaced by Guile.