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: A jungle girl is found. She has been lost in the wild since she was a little girl. She must get regular visits from the Avon lady because she has on perfect makeup including lipstick.
Other mistake: After the crash landing in the desert, when the astronauts are preparing to head out on foot, Brubaker states that he will continue west, then tells Walker to go north, and Willis to go south. Brubaker heads out straight ahead, Walker goes to the left, and Willis to the right, meaning that Walker was actually going south, and Willis to the north. (01:04:40)DavidCBohn
Other mistake: When we see the county sheriff's station wagon pull into the cafe parking lot, it has a California license plate instead of an Oregon "state vehicle" plate.