On the title screen and title menu screen, if the player presses left on the D-Pad then Takayuki will smoke the cigarette he has in his hand.

Some of the names of the Arcade Shop missions in Lost Judgment which are unlocked through playing Sonic the Fighters are references to aspects of the Sonic franchise.

The missions for beating Sonic, Tails, Knuckles and Amy are all named after their themes from Sonic Adventure or Sonic Adventure 2: Live and Learn, Believe In Myself, Fighting Freak and My Sweet Passion.

The mission for beating Fang the Sniper is titled Knack For Trouble which could be a reference to both Fang's original Western name Nack the Weasel as well as his debut game Sonic the Hedgehog: Triple Trouble.

The mission for beating Bean the Dynamite is titled Mean Bean Machine after the 1993 Sonic-themed Western localization of Puyo Puyo, Dr. Robotnik's Mean Bean Machine. Ironically, Puyo Puyo did not appear in Lost Judgment despite being in it's predecessor, Judgment.

Finally, the mission for beating Espio is titled Chameleon Detective after Espio's role as a detective starting with Sonic Heroes. It could also be a nod to the Lost Judgment's protagonist Yagami being a detective who often needs to don disguises to blend into places.

Unused animations for Ichiban Kasuga riding a skateboard exist in the data for Yakuza: Like a Dragon, suggesting he was intended to get around the world map on a skateboard at one point. Skateboarding would later be implemented in Lost Judgment.