Why was the alien hanging the humans in his cave? Why don't the humans wake up when the alien grabs them in his huge claw, but the girl wakes up when she is slapped by the candy wipe boy? Why does the army keep firing their weapons when they don't work and fly into their own forces? Why didn't the alien breakout of the train before the crash? How did the "Doctor teacher" survive the train/truck wreck ( I mean c'mon that truck would have been a flattened, charred ball of smash)?
100 more logic questions waiting to be asked/answered.
edit:
and it goes on...
Some examples: how can a small pickup truck derail a high speed freight train? How can the driver of that truck still remain alive? Why would 8MM raw footage of an alien be edited together with a well recorded voice over? Why, when the train first approaches, does the kid yell "production value" but he never repositions the actors to show the train in the background? Why are the aliens cubes in trucks near the water tower when the Air Force knows the alien needs them for his space ship? When they have the big town meeting, where is the press and national news? When the kids are running through town, why is the Air Force blowing up everything in sight? And when the Air Force speeds to the train wreck they see a car drive away, but instead of chasing the car they just decide to check the tire tracks and match them (which never pans out).