Continuity mistake: When Flint's dad is looking out of the windows of the door to his shop as the food starts to rain down, the text and words on the door that were there earlier in the film have disappeared.
Other mistake: When the mayor is talking behind the chainlink fence, with Brent in the background eating sardines, you can see as the mayor grabs the fence, his thumbs clip through the fence wire. This occurs on both hands and easily visible, particularly when Mayor Shelbourne says, "Otherwise, I'm just a tiny mayor of a tiny town full of tiny sardine-sucking knuckle-scrapers." (00:10:52)
Suggested correction: This isn't really what happens, although it looks like it does. The mayor's thumbs are not pointing outwards, they are curled around the fence wire. As he continues to grab the fence, his thumbs don't clip through it, they curl more and more around it, getting a tighter grip on it. Then when Brent says, "But not me, right?", he lets go, and you can see his thumbs curl back out. This is all visible if you look close enough.
Plot hole: There is no possible way for the chubby mayor to be able to get in Flint's lab. There is no side entry, and the space other characters use to get in is too tight for him.
Continuity mistake: After the spaghetti twister, Flint puts on his lab coat in the elevator and you can see he has his tuxedo shirt on. Then during the building montage, it's a blue shirt, then changes back to the tuxedo shirt when he turns on the car. Also, during the building, the design on the blue shirt disappears.
Continuity mistake: When it's Cal's birthday, in the first shot of the ice cream truck thing, look at the children on top of it. They all are facing different directions. When you see the close up of the ice cream crushing them, they are all facing to the left.
Continuity mistake: When the giant fishbowl is launched into the air it's about 1/3 full of water. However, when it lands on Flint, it's completely dry. Even if most of the water got tossed out(which is unlikely), it should still be dripping pretty hard.
Continuity mistake: Before the Ice Cream Snow scene you see Cal wake up in his bedroom with his pajamas on, in the very next shot, when he sees the ice cream outside, he has his coat on.
Continuity mistake: In the scene where Flint has been persuaded by the Mayor to keep the machine running and is about to enter the food code, it changes to a shot showing his computer screen. in this shot, his computer is using Windows. But in the shot of the same screen where Flint's Father is about to send him the kill code, the computer is using a Mac OS. (00:45:35 - 01:08:05)
Continuity mistake: When Flint first discovers that it's raining food, in the shot where you hear Steve saying "Excited", Flint's jacket isn't moving at all in the wind. It does in the close-up.
Continuity mistake: On the dock, in the shot of the clouds, you can see about 100 hamburgers aimed for the dock (the middle). Yet at the end of the scene when Flint says, "It really works!" only 20 or so hamburgers are visible on the dock. The wind was moving south as seen by Flint's coat blowing in the breeze, so the wind couldn't have blown them in the water. Also, the fact that we see one more shot of the clouds and the burgers (with about 200 more aiming for the dock) makes this impossible.
Continuity mistake: When Flint, Steve, and Sam are on the dock watching the burgers fall, Flint reaches out and catches a burger. To his left (your right), one can see a busted cheeseburger. Later, when Flint yells,"it really works!" part of it has disappeared.
Plot hole: When Flint gets to his lab to shut down the machine he finds the mayor there inputting more food. The mayor says he's been ordering food for ten minutes, how is this possible when he was just there with Flint on the stage barely a minute or so before? Also, how did the mayor manage to get his large self back to Flint's lab so quickly?
Continuity mistake: When Flint sneaks out of the shop, he runs past the ceremony and hides behind a pillar. Nothing can be seen of him, but when the camera pans to Flint, some of his hair can be seen peeking over the pillar.
Other mistake: When Flint configures the computer to rain breakfast, he types the eggs as "over easy". However, when breakfast falls, all of the eggs are sunny side up. This is not likely an error of his invention because in every other case it produces the food exactly as he inputs it.
Revealing mistake: When young Flint is showing his class his Spray-On Shoes we see the shoes of the class with their untied laces but when the camera is moving towards Flint from behind the class none of the laces are dangling.
Continuity mistake: Little Flint makes a drawing and sticks it between two of his posters. In the first shot the left corner is by the "M" of "Graham", but in the overhead view it's on the second A. (00:03:00)
Revealing mistake: When Flint screws the fuse into the fuse box to get the lights back on his dad just appears out of thin air.
Continuity mistake: In the beginning no-one's shoes are untied, then it shows you they are, and after that they're tied again.
