It's possible to shoot down the World Government's flag on top of the Tower of Justice with Usopp's Fire Bird Star. It's the only destructible flag in the Enies Lobby level, and doing so in the PlayStation 3 and Vita versions will earn the trophy, "Declaration of War".

Hidden within each area, Pandaman can be found hiding in inaccessible areas of the map. He also appears in the form of a rarely spawning balloon in Trans Town.

The description for Punk Hazard usually reads, "The land of ice and fire. A difficult battle awaits in this hostile environment." In the US 3DS version however, the description reads, "Beware the tear-inducing assault it unleashes when cut. Cook it to draw out its natural sweetness.". This seems to be a glitch where the game replaces Punk Hazard's description with that of the Super Onion's description. This glitch is only found in the 3DS version.

Through the use of hacking, unused items called Pandaman Red, Blue, Yellow, Green, White, Black, and Gold can be found. Why they were removed is unknown, but odds are they would have been items hidden in areas that match their colors.

The US box art for the game was slightly altered to cover up both Nami's and Robin's chests.

The version of Crocodile in the game is based off his Impel Down/Marineford appearance, but his sleeves are incorrectly colored white.

Patrick Redfield, Pato, and Yadoya were all personally designed by One Piece creator Eiichiro Oda.