Continuity mistake: When they first see the crop circle, Graham takes one step into the area, and the rest of his family crowds behind him, still basically in the corn. In the next shot (arial shot), supposedly right away, Graham is about ten steps into the circle, while Morgan and Merrill are about six or so. (00:05:00)
Continuity mistake: After the incident with Houdini, when Graham picks up Bo from the play house her right shoe is untied. When he is seen carrying her into the house the shoe is properly tied. (00:10:30)
Continuity mistake: When the deputy sheriff comes out of the house, her ink pen is sticking through the hole in her pocket flap but not in the pocket itself. After she turns around at the car, her ink pen is inside her pocket and not "flapping" loose as it was just a split second before. (00:21:15)
Continuity mistake: In the scene where Merrill, Graham and the kids are returning home from town, and Morgan is holding his baby monitor to listen to the aliens, his fingernails are very long. When he gets out and climbs on top of the car to get a better listen, his fingernails are very short. (00:29:55 - 00:32:15)
Continuity mistake: When Graham goes into Ray's kitchen you see the vegetables scattered and the knife further on the other side of them. When Graham leans up for the knife, however, it is on the other side of the now grouped vegetables. (00:56:40 - 00:58:10)
Continuity mistake: When Merrill aims at the alien for the final blow he is shown looking upwards as if the alien were looming over him. When the camera angle changes he is looking straight at the alien in front. (01:33:00)
Continuity mistake: When Merrill delivers the final blow to the alien, you see it fall into a table and knock over a single glass of water from the alien's perspective. In the next shot, the top of the table is shown with three tipped glasses. (01:37:40)
Continuity mistake: In the scene where Morgan is explaining what the aliens would do if they were hostile (when Morgan, Merrill, and Bo are wearing tin foil hats), Merrill is seen hugging his knees in a closeup shot. In the next shot, Merrill has his hands on top of his knees now, instead of hugging them.
Continuity mistake: When Graham takes the knife off the cutting board and is holding it, it does not have the perfect mirror on it as it does when he looks in it or is using it to look under the door.
Answer: It's left unclear, though the film proposes several possible theories, and there are other possible explanations as well. One major theory brought up in the film is that the aliens were there to acquire Earth's resources after using up their own. Another theory proposed at the end of the movie is that the aliens wanted humans for whatever reason, as a radio DJ mentions seeing his friend's family being dragged away. There is also a very popular fan theory that the aliens are supposed to represent demons that are merely there to create chaos and test the moral strength of humanity, as the film is ultimately about Graham losing and then regaining his faith, although this is more subtext than anything and may not be literally true.