Yakuza 3 features an unused remix of a song called “Bruise” in the game files, originally intended to be used in tag battles in the Coliseum. This song would later be used in-game in Like a Dragon Gaiden: The Man Who Erased His Name in 2023.

Kaito, Sugiura, and Makoto from the Judgment sub-series make cameo appearances in the games Like a Dragon Gaiden: The Man Who Erased His Name, and Like a Dragon: Infinite Wealth. Despite this, Judgment's main protagonist Takayuki Yagami has never made a cameo in the Yakuza series. This may be due to the fact that his face was modeled after his voice actor, Takuya Kimura, who is a popular celebrity in Japan and could be expensive to license out.

The game features cabaret club minigames with fully live-action cutscenes instead of the usual 3D animated cutscenes. This ended up using a massive amount of storage, and Ryu Ga Gotoku Studio's technical manager Yutaka Ito estimates it to have taken up 77% of the game’s total cutscene data.

There is seemingly an error in the descriptions of the Daidoji Grapple Strike/Grip Breaker moves in both fighting styles. The moves are simple counters for if Kiryu is grabbed, and act as a way for Kiryu to throw the opponent off of him. However, the descriptions for the moves read "When surrounded by enemies", implying a different function for the move.

A common theory is that the character Hanawa, Kiryu’s handler from Like a Dragon Gaiden: The Man Who Erased His Name, is actually Yu Morinaga from Yakuza 5. This is because Spoiler:Morinaga was killed off-screen and his body was never shown, the character has the same voice actor as Hanawa, and he calls Kiryu "Taichi Suzuki", which is the codename he goes by in Yakuza 5.