An unused animation of a lured Cog, depicting it moving left and right, can be found in the game's files.

Photo Fun, a mini-game that appeared within the trolley, was removed in February 2011. It was removed due to a bug that would cause the game to crash on most Mac computers. The files for the mini-game can still be found within the game's data.

During the game's Beta, cogs were called "The Suits".

Goofy could be found in Daisy Gardens until the gardening and racing activities were released.

During the game's beta, there was a glitch that allowed Toons to have colored gloves. However, performing the glitch would have the user's account terminated.

During the beta of Toontown, Donald Duck wore his normal sailor outfit instead of his pajamas in Donald's Dreamland, and was not sleepwalking.

During the game's beta, a character's Toon Laff could only go up to 100.

Prior to 2007 when they were changed to green, Toons originally had orange name tags.

There is an extended version of the crying emotion sound never used in the game.

The Japanese version replaces the noises that accompany text dialogue with full voice acting which reads out the dialogue.

There is an unused animation for an attack where a cog smokes what would likely have been a cigar.

There is an unused animation of a cog's feet walking away after the body is blown up.

The original flash launcher of the game, shown while the game was downloading, included an animation about how the cogs were made.

The story was that Scrooge McDuck visited Gyro Gearloose but didn't find him at home, he then found a robot and tried to repair it to make a profit, the robot in turn then created the cogs with another machine found within the lab.

Despite being an online-oriented game, Toontown Online was briefly distributed as a CD-ROM title in 2005, with Sony subsidiary Platform Publishing handling the physical release. The CD-ROM version allowed players to run the game without needing to install it onto their computers and came with a free two-month subscription and an in-game kart that players could drive on Goofy Speedway. Home console ports of Toontown Online were also announced concurrently with the CD-ROM edition, but these never materialized.

According to a 2004 Game Developer article by developer Mike Goslin, the decision to give the game a physical release was due to anxieties from consumers about not being able to physically hold a game that they were spending money on, as online distribution had not yet been fully established as a mainstream distribution model for video games.