Just before they land, Adams impatiently flips off the radio as Morbius is in the middle of the word "recommend". Morbius should have been cut off immediately and in mid-word. But we hear him say the full word "recommend" even after Adams has shut the radio off.
While the three men are standing on the walkway in the Krell machine, Morbius points to his right and says "Twenty miles". He then points to his left and says "Twenty miles". Since the three would then seem to be in the center of the machine, that would make it forty miles in total width, yet in the in the second scene following, he states "Yes, a single machine. A cube twenty miles on a side.". If it is indeed a cube, as Morbius indicates, the Krell machine shrunk from 64,000 cubic miles to 8,000 cubic miles in a little less than half a minute - Quite an error for a scientist with an expanded mental capacity to make.
As the vehicle driven by the robot first drives up to the residence, there is a tow cable visible in the foreground, partially obscured by the bushes. This cable is most visible behind the vehicle as it leaves the scene.
When the Monster is burning/melting the metal door, as it turns white hot and lumps start to fall, you can see a member of the crew in a heatproof suit prodding the material from behind to make it fall. Watch the second and third holes for movement behind the door. Then again, this motion could be taken to be the monster doing the poking...
When Robby the Robot carries the Doc out of the study after the latter has taking the brain boost, wires can be seen suspending the Doc from the ceiling. The actor inside the cumbersome robot costume was obviously not able to support the Doc's weight.
Robby the Robot shows up carrying lead shielding, which he says is "isotope 217", and he implies it is lighter than ordinary lead. The purported isotope lead-217 does not exist, and if it did, it would be 4% heavier than the most common (and heaviest) isotope of lead (number 208), not lighter.
The star Altair is shown as an orange-red star, eclipsed by one of its (spherical) planets. It is now known that Altair is white and is oblate, with its equatorial diameter 14% greater than its polar diameter, something that was not known when the movie was produced.
The monster leaves a flat footprint, yet the cast of the footprint shows a huge curving claw and other three dimensional structures that could not possibly have been gleaned from the outline of a flat footprint.
As Morbius shows the Commander and Doctor around the Krell underground complex, sometimes they cast shadows on the ground and sometimes they do not. Also at one point their reflections can be seen in puddles of (rain)water lying on the surface on which they are walking.
In several wide shots of the crew members outside the ship, there is a faint vertical shadow visible on the painted backdrop behind the ship. It appears to be either a fold in a piece of fabric or the corner of the sound stage wall.
After Robby the Robot short circuits due to logic conflict between obeying Morbius (ordering him to destroy the monster) and knowing that destroying the monster (id of Morbius) would destroy his master, just before the shot ends after Robby is supposedly immobile, his arms wiggle.
Two visible glitches in the last scene in the film. As Adams and Altaira stand watching the view screen as Altair-4 explodes, the shot of the couple abruptly freeze-frames while the Altair explosion is shown. Immediately after, in the close-up of the two embracing, there's a visible cut in the film and the pair (plus the Bosun in the background) slightly shift in position.