The North American PlayStation 2 Greatest Hits re-release of the game was originally printed with The SpongeBob SquarePants Movie logo mistakenly absent from the front cover, though this was corrected with later printings.

Normally, the player is required to defeat the MERV enemies in "Welcome to Planktopolis... Minions" either with the Sonic Wave Guitar or by deflecting their missiles with the upgraded Karate Spin. However, they can also be attacked by walking directly underneath them, which deactivates their lasers and allows SpongeBob to hit them with the Bash. This typically goes unnoticed in normal gameplay, as MERVs' lasers try to repel the player if they get too close; additionally, the Mini-MERV enemies encountered earlier in "Shell City, Dead Ahead" instantly repel the player if they get even closer, meaning that there would be no opportunity to discover this alternate strategy in advance.

In 2012, The SpongeBob SquarePants Movie was ported to the PlayStation 3's PlayStation Network under the PlayStation 2 Classics line. However, it was taken down shortly afterwards with no official explanation. Audiences quickly inferred that the port's withdrawal was due to the poor reception it drew thanks to various emulation issues involved with it, though it may have also been due to THQ going bankrupt and Activision acquiring the license to make games based on Nickelodeon properties around the same time. Among these emulation issues, the 16:9 display (which was the default option) stretched the game rather than properly re-rendering it at a higher aspect ratio, the audio for in-engine cutscenes frequently stuttered and fell behind by up to a second, certain textures were noticeably blurry due to the game being displayed at a higher resolution than what it was designed for, and gameplay suffered from prominent input lag compared to the original release.

In the level "I'm Ready, Depression...", attacking the organ will cause it to start playing music.

If the player goes into a secret area in the level "Welcome to Planktopolis... Minions", they can see Heavy Irons timed records for the slide and racing levels.

Heavy Iron Studios were the development team for the game.

Patrick's model has "Goofy Goober" underwear, but it's always hidden under his shorts. It's possible to see it via bugs and glitches.