Other mistake: One visual that has always bothered me that I could not find in your list were the scenes when the mother ship first appears. It's enormous scale appears to dwarf Devil's Tower and the whole surrounding area actually, but when it moves over to the "landing strip" area and begins to rotate 180° (right-side up?), it suddenly seems to shrink to a much smaller size and mass during the slow revolution. On its originally-seen scale above/behind the tower, one would think that either the great ship's outer prongs would have been torn off, or more likely the impromptu landing site and most of Devil's Tower would have been destroyed as the huge craft rotated itself. The visual scales just do not stay consistent throughout the film's climactic final act.
Other mistake: In the climactic scene at the end of the movie when the alien mothership flies over Devil's Tower and the base, there is a shot of the mothership's shadow creeping along the ground, enveloping the shadows of the crew there. It's a dramatic shot, but since the mothership was not between the ground and the light source (the stadium lights of the base) it should not be blocking out the light, or creating a shadow. (01:55:08)
Other mistake: When Richard Dreyfus rushes to the street to grab the trash can as the trash truck is coming down the street, his family is the only one on the block that has their trash cans out. It's obviously trash day and many of the houses are yet to be serviced by the approaching trash truck. (01:14:30)
Chosen answer: I own the original (not special edition) DVD and I can always freeze the film and point out to people where the alien is and they see it too, but I can never see it when it's on TV or on my friends VHS copy, maybe it's just a 'gift' for the DVD owners?