In the wind machine, when Sam goes up to the big fan, the yellow flags alongside the walkway that are blown by the fan disappear.
In the path where Sam rescues Wingnut from the drain, he must shrink himself down using the "Shrink-O," get Wingnut, and then go back to his normal size to put Wingnut back. Wingnut didn't pass through the Shrink-O when he was shaken loose, so when Sam goes through the Shrink-O to get back to his normal size, Wingnut should be larger as well (and thus, too big to go back onto the sun machine).
Sam may have to get either the Y-pipe or a bag of Cheese Giblets out of the vending machine in the lunch room. In the long shot of the lunch room, the buttons on the vending machine are square, there are nine, they are above the coin slot, and they are just out of Sam's reach (near the top of the window of the vending machine). However, in the close-up of Sam putting coins in the machine, the buttons are round, below the coin slot, there are six, and they are near the bottom of the window of the vending machine. Also, the close-up shows a display and a yellow-orange stripe that weren't present in the long shot.
A weather factory keeps "earthquake in a can" in the basement. Earthquakes are not weather - they are not caused by the sun. They are caused by tectonic plate movements.
The rainwater in the weather factory is made from H2 (hydrogen) and O (ionized oxygen). While this makes the chemical formula of water (H2O) easy to understand from a child's point of view, it is just not how water is made from hydrogen and oxygen. Oxygen, like hydrogen, is a diatomic gas, meaning it only exists as O2. The actual reaction that produces water takes in two H2 molecules, an O2 molecule, and it gives two water molecules (2H2O).
World Wide Weather has a "no visitors" rule, as the gate says. However, when Sam gets in, and he first meets the courtesy phone, the phone says "welcome to World Wide Weather, sir!" as if WWW didn't have such a rule. Come to think of it, this rule is only mentioned by the gate.