(at around 24 mins) When Flint is explaining how the machine can turn water into any kind of food, Sam asks if Jell-O is possible. Flint says yes, and then asks if she likes peanut butter. Sam says she is extremely allergic to peanuts, which prompts Flint to say, "Oh yeah, me too!" In real life, Bill Hader is highly allergic to peanuts.
According to the director's commentary on the DVD, Earl was going to be a gym teacher and part-time cop. His profession was changed to a full-time cop only, but they kept the gym teacher's short shorts on him.
(at around 4 mins) The island on which the town of Swallow Falls (later Chewandswallow) is located corresponds to the real-life geographic location of Bermuda. This is implied at the beginning when the island is said to be under the first "A" in Atlantic, as Bermuda is the only island in the West Atlantic north of the tropics. It is later confirmed on a weather map towards the climax of the movie (at around 54 mins), when the weather storm is clearly seen to originate several hundred miles of the coast of the Carolinas.
(at around 28 mins) In one scene, a rainbow of little colored bite-sized candies ends in children's mouths. This is a reference to Skittles, a fruity bite-sized candy whose slogan is "Taste The Rainbow".
The directors originally wanted to get Electric Light Orchestra's title song from Xanadu (1980) to play under the end credits, but they couldn't find out who owned the rights. Miranda Cosgrove's "Raining Sunshine" was used instead.
This was the first Columbia Pictures/Sony Pictures Animation film to have an altered logo sequence. When the Columbia Pictures logo appears, a banana hits the Torch Lady and knocks her out of the image. During the Sony Pictures Animation logo sequence, dark clouds uncover the end of the logo.
(at around 7 mins) When Flint tests the Food Replicator and the power goes out, the musical score stops. However, the tune Flint is humming as he leaves the lab to fix the circuit breaker is the melody of the musical score.
(at around 38 mins) After "The Reveal" Flint removes his hands and gets a good look at Sam. Then his eyes seem to get bigger because his pupils dilate. It has been proven by scientist that a person's eyes dilate by 45% when they see something they love, just proving the fact that Flint loves the nerdy side of Sam.
(at around 57 mins) When Flint is in his lab "visualizing" with the 3-D holographic images, he's wearing glasses with red and blue lenses. The glasses are a nod to the original 3-D movies from the 1950s to the late 1990s which required glasses with red and blue lenses in order to make the 3-D effect. Nowadays, movies such as this film use a different form of 3-D technology that uses "polarized" rather than colored lenses.
The trivia item below may give away important plot points.
at around 1h 13 mins) As Flint is flying in his 'Flying Car 2,' giant gummy bears attack the vehicle and begin tampering with the wings. This is a reference to Star Wars: Episode III - Revenge of the Sith (2005) when buzz droids do the same to Obi-Wan and Anakin's ships.