During the dance scene, John Cusack is wearing a WLS t-shirt. Although it changed to a talk-radio format in 1989, WLS was a top-40 music station in Chicago at the time this movie was filmed.
When Jake Ryan goes to Sam's house looking for her, and Long Duk Dong answers the door, the hot water bottle Long is holding moves from the top of his head to the side of his neck, and back.
When Jake puts Caroline in the Rolls-Royce, he clearly puts her legs inside the car. Yet before he lets Ted leave he puts her legs in before he shuts the door.
In the opening sequence, a geek is having trouble opening the pad lock on his locker. When the locker is finally opened, some of the objects that fall out are obviously falling from overhead and not from the locker.