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.
Factual error: Most of the parachutes are PX type. These came out in the 1960s. They only used X type during the war - only a few of those are seen in the film. (00:07:00)
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: Sheriff Buford T. Justice gets out of his car and leaves the door open. A few moments later, we see a different shot of the car with the door closed. Then a truck drives by and tears the car door off which is open again.
Continuity mistake: Richard Dreyfus comes home drunk after his horrible opening night. He stumbles around the living room knocking over furniture, including a table by the window with a typewriter on top. Next time you see the table, it is all together again.
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.
Continuity mistake: A shot of the chiefs' bench shows Newman on the left and Ontkean on the right. Ontkean says "I can't believe my frigging eyes." Neither can I. The next 2 rapid camera cuts show Ontkean on Newman's left, then on Newman's right again.
Factual error: After the plane is submerged, Jack Lemmon says, "... this plane is pressurized!" Jet aircraft are pressurized by bleeding air from the compressor sections of the engines into the cabin; in other words, the plane is only pressurized while the engines are running. Also, aircraft are only pressurized to a few psi above the outside air pressure at altitude, and never to more than the air pressure at sea level. The water pressure would be a great deal higher than the air pressure in the cabin, and since aircraft are not water tight, the water would quickly fill the aircraft. (If the aircraft was in 50 feet of water, the water pressure would be 21.7 psi, versus a maximum cabin pressure of 14.7 psi.)
Continuity mistake: When the blonde girl is persuaded to talk to the Trogladyte, in different shots, her hair is either over her shoulders, or off her shoulders.
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.
Continuity mistake: During the car scene, when God makes it rain, Jerry's hair goes from being dry to wet, repeatedly, depending on the camera angle.
Continuity mistake: When the crew hauls the female orca aboard the boat, the harpoon line is wrapped around her entire body several times. When they cut the rope and drop her into the water, the line is wrapped only around her tail. When the male orca is pushing her at sea, the rope is again wrapped around her entire body.