Other mistake: When the stormtroopers break into the control room, the stormtrooper on the right of the screen hits his head on the door frame. On the DVD release they've added a thump when he hits it. (01:18:55)
Plot hole: The "death" of the three astronauts and the requirement to then fake the whole scenario of the failed mission was obviously unplanned - it came about because of an unexpected computer glitch which reported that they had burned up on reentry, causing a mad scramble to cover up the fake mission and kill the astronauts. Obviously it was planned to have the astronauts "return" to Earth as heroes after their supposed trip to Mars, maintaining their deception (under threat if necessary) for the rest of their lives. One problem. Every scientist on earth would be champing at the bit to get their hands on a sample of Martian rock. Samples would be worth billions, worth far more than Moon rocks are worth today. How was NASA going to explain they didn't have any? They could not possibly fake the rocks - Martian soil and rocks would have a number of identifiable characteristics that a smart first year college student could identify. Using Martian meteorites collected from the Earth's surface won't work, either - prolonged exposure to the Earth's atmosphere would leave tell tale weathering and chemical changes that would be instantly detectable. NASA have painted themselves into a corner and that is not something they would have failed to realise well in advance.
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.
Continuity mistake: In the story titled "Quebec Province 1975", child witch Lucy gets back at her bullying cousin Angela by shrinking her to the size of a mouse. Minutes later, Angela looks up, lifts her hands over her head and begs for mercy. Obviously Lucy is preparing to step on her. But we see Lucy lifting her foot off the floor several seconds after Angela starts begging.
Revealing mistake: At one point in the movie, dumptrucks are sent in to contain the Mighty Peking Man. You can tell that these, like most of the movie are toys.
Visible crew/equipment: During the opening scene when the boat is being pushed ashore you can see the shadow of the boom mike in the water's edge.
Visible crew/equipment: When the camera is pulling back really fast being chased by the people in Africa, its shadows can be seen multiple times on the characters and the walls.
Continuity mistake: The senator is tossed out of the boat and consumed (with the exception of his head) by the monster, and yet the boat is full of blood.
Continuity mistake: The spider lady and the vet go to the rancher's place to burn out the spider hill. While there, a bull runs out and collapses. While the spider lady is talking to the rancher's wife, her hands are by her side. When the camera switches to the wife's point of view, the spider lady's hands are in her coat pockets. When the view switches back, her hands are by her side again.
Suggested correction: They could use meteors that had landed on Earth. This is one of the theories for the "faked" moon landing, that they either created the moon rocks from scratch, or collected meteors. As for the death of the astronauts, that's not a plot hole, it's the plot of the movie; the powers that be wanted the men to fake everything and return as heroes. When they wouldn't play along, it was decided they needed to be eliminated.
It is clear from the narrative of the film that it was planned that the astronauts would "land" safely. Using meteorites would not work - exposure to the Earth's atmosphere would mean (and has meant) that the rocks would show weathering and chemical changes that anyone would be able to detect.