In the English localization of the main game, the Marines are referred to as "Navy", with the civilian Pro-Marine and Anti-Marine factions being renamed "Pro-Navy" and "Anti-Navy" to reflect this. However in the "The Unfinished Map" DLC, they are simply referred to as "Marines" once again.

In the Japanese version of the game, the opening cinematic features the song "Kimi no Moto e" by Ketsumeishi. Due to licensing issues, the song was replaced with "Road to Ichiban" from the main game in the international release.

The Germa 66 Raid Suit DLC for Luffy is a reference to the color spread featured in Chapter 872 of the One Piece manga.

In the "The Void Mirror Prototype" DLC, Roronoa Zoro's map and minimap are heavily pixelated, making it harder for the player to know where they are going. This is to simulate Zoro's lack of orientation in the series.

The pose the Strawhat Pirates make in the post-credits scene is a reference to the cover of volume 61 of the One Piece manga.

Throughout the game's map, Pandaman can be found in inaccessible areas.

In the Japanese and European versions of the game, a DLC quest was released called, "The Phantom Remedy" which had Luffy visit a nearby island with a hot spring. The quest would task Luffy with collecting bottles to gather water from the hot spring, as it's rumored to grant eternal youth. Each time Luffy would visit the hot spring, he would come across Nami, Nico Robin, and Tashigi bathing in the springs.

This DLC was not made available in the North American release, though the island would later be patched in without the quest.