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.
Factual error: As the divers surface, they inform the sheriff that the meteor, despite having landed in a lake the night before, is so hot that it may take weeks to cool off.
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.