If you add the line "EddieEatsLuther=1" to the hegames.ini file and click on Luther after meeting Eddie the Eel, a hidden cutscene will play where Freddi will feed Luther to Eddie. Freddi will then turn to the camera, wink and stick her tongue out, before cutting back to Luther right next to Freddi who asks "Whatcha thinking about, Freddi?" who replies "Oh, nothing, Luther.". It's believed this cutscene was never meant to be seen in normal gameplay and was simply a way for graphic designer Tom Verre to let off some steam.

If you are using the game outside of the original ScummVM engine, you can find the area to activate this cutscene within the "HEINI" file on your system. In the box labeled "Key", type "EddieEatsLuther" (one word, case sensitive, no quote marks) and under the box labeled "Value" enter 1.

In the "HEINI" file, you can also enter "BretIsTheOverlord" (presumably referring to programmer Bret Barret) in the "Key" box and like before enter 1 in the value box to see this cutscene multiple times, or else EddieEatsLuther will be unable to be activated after the first time you see it, even if you restart the game.

In the junkyard area, after you give the dog fish a bone, you are allowed to go inside a purple car to retrieve a speedometer. The car may be a gruesome nod to Putt-Putt. Other than having a roof, the run down car shares many similarities with Putt-Putt, such as similar designs, color, and even a similar looking dashboard that's inside. The Putt-Putt series was also made by Humongous Entertainment.

The 2001 Norwegian version of the game not only colorized the item cursors , but also made the movement animations skippable, which didn't happen in any other region until the 2007 rerelease.

Pajama Sam: No Need to Hide When It's Dark Outside and Freddi Fish and the Case of the Missing Kelp Seeds were released on the Wii as Pajama Sam: Don’t Fear the Dark and Freddi Fish: Kelp Seed Mystery respectively, alongside Spy Fox: Dry Cereal, which kept its name. However, these ports ran off of the ScummVM emulator engine and did not use proper attribution, leading to all unsold copies of the games being removed from sale and destroyed, and mandatory donations being made to the Free Software Foundation.

The Case of the Missing Kelp Seeds was the first Humongous Entertainment game to use cel animation instead of computer-designed sprites. This was a last second choice that required all existing visuals and much of the game's code to be thrown away, and was done without a delay nor much in the way of cel animation knowledge from the team, requiring unpaid overtime. Despite this story's surface-level similarities to crunch practices, the challenge of remaking the game on such short notice was chosen and consented to by the Freddi Fish team, and developers of the game have reminisced on this period fondly.