About an hour into the movie, when the helmsman says "Now in fourth quadrant", his mouth says something different and moves considerably longer. The same thing is happening again about two minutes later, when he announces "Entering ionized layer".
In the scenes from the formal dinner to when Cal and Ruth are taken aboard the alien spacecraft, Ruth's attire keeps changing. Initially she is wearing a white cocktail dress with an off-the-shoulder neckline, and no jewelry. Later her dress has a higher neckline and she is wearing a pearl necklace. Still later, the necklace is gone again, the dress has returned to the lower neckline, but it now appears to be a pale lavender color. In at least one scene she seems to be wearing a blouse with a darker skirt.
When Dr. Mecham is in the lab after he returns from Washington, his assistant says he ordered two XC condensers and he got two "beads" in the mail. He said he had tested one and it blew out at 33,000 volts. Dr Mecham says let's test this one. They test it and it disintegrates at 35,000 volts. But, Dr. Mecham still has one in his hand and they try to drill it, etc. If they only received 2, and blew both of them up testing, where did the 3rd one come from?
When the space ship returns from Metaluna, Exeter tells Cal and Ruth to get in the airplane because they were in the Earth's atmosphere. The next scene shows they were obviously well outside the atmosphere.
As the ship leaves for Metaluna, Earth is shown on the view-panel, becoming smaller very rapidly. Yet several minutes later, the ship is shown becoming very hot, and Exeter says they are going through a "thermal barrier". Then there is discussion of leaving Earth's gravity. Both of these events would have occurred long before we had seen the Earth become so small on the view-panel.
When Faith Domergue and Rex Reason first enter their new lab
and see the orange cat, Faith tells Rex that the cat is named "Neutron" because "he's so positive". Any scientist, especially a nuclear fission expert, should know that a neutron has no charge, and that it is the proton that is positive.
When Cal is going to take off from Washington DC, the aircraft he is flying is a T-33. During the interview, the planes type and other data is clearly visible on the aircraft. The plane shown taking off is not a T-33 - it has a different type of nose.
When the two doctors are aboard Exeter's ship, their hands grasp the metal bars, and Exeter said they did because the bars were magnetized, which might mean something if human hands were made of metal.
When Cal and Ruth are on the ship, some of the aliens are leaving the compression tubes in preparation for Metaluna's atmosphere. Cal and Ruth then go into the tubes to undergo the same process. But, if Cal and Ruth were not yet compressed, and the aliens were, they should not logically be able to be in the same room at the same time, as the pressure would not be hospitable to one group or the other.
No one, not even the humans, seem to consider that Zagons would eventually come to Earth. The Metalunas, including Exeter, don't even suggest that this is a good reason to work with them. Once Metaluna is gone, it seems to be the end of it.
When Cal Meacham is asked to move the lead slab closer to the Interocitor, prior to Exeter burning a hole through it, a circular, discolored area can be seen in the center of the slab where the special effects incendiary cap is concealed.
When Exeter is first talking to Dr. Meacham and Adams in his office, he shows them his Interocitor which is located in a large closet next to the door into the hallway. The closet's door is flush to the wall with the office door, but when they are out in the hallway, the outside wall is also flush, which means there was no place for the Interocitor in his office.