Deliberate mistake: When Elliott and ET are on the bike heading to the forest on Halloween night, ET is covered with the white sheet, but in the closeup of ET's face right before the bike flies he's covered with the white blanket (note the material), which is from the scene later in the movie.
Deliberate mistake: The text the Master Control Program speaks in the human world is usually accompanied with a text projected on a computer screen. When Flynn attempts to hack into the system through the laser lab terminal, the Program is cut short at 'I'm afraid you.' (both on the screen and in speech) as Flynn progresses. In reality, however, it should be that the full text intended to be relayed by the MCP should be displayed on the screen, and only the speech gets interrupted. (00:29:40)
Deliberate mistake: When the security forces arrive at the hangar to report seeing Gant at security gate 3, they are driving an American Jeep.