Other mistake: When Joe picks up one of the cubes and puts it in his jacket pocket, Charles is nowhere around him. Later, Charles tells Joe that he told him not to touch it [cube] in the first place.
Audio problem: The train horn sound changes from what it was to a different horn sound when it passes the Lillian Depot. Then it changes back. (00:16:30)
Continuity mistake: When the kids break into the school and discover the footage of Dr. Woodward and the other scientists, they break a window on the classroom door. The glass is almost completely removed from the frame but once the military arrive and take the kids away, there is suddenly more glass in the frame. (01:14:50 - 01:17:25)