When Doctor Smith revives Major West from suspended animation, he takes off the Major's right hand glove to attach a type of reviving mechanism. When West wakes up, Smith drags the groggy West to the flight panel so West can fly the ship. When the camera looks down at Major West's hands controlling the flight stick, he is shown wearing gloves on both hands not one.
When the narrator is giving the "guided tour" of the ship near the beginning, the view is given from the elevator platform as the elevator descends to the lower deck. The view pans across the lower deck and the Robot's station, but (as the shot is from the original pilot which did not include the Robot) the Robot is nowhere in sight. The narrator then mentions the Robot and a view of the Robot is shown with the elevator in the background. The shot then changes back to the view from the platform and pans back across the lower deck. The Robot is again missing, even through the floor markings where his station is placed are shown.
When Smith is calling on the handheld radio after launch, the elevator tube behind him does not show the elevator platform, as it is on the level above. When he hears the Robot's circuits operating, he looks towards it and the view of the Robot shows the elevator platform in the down position behind it. The shot cuts back to Smith, and the platform in no longer visible in the down position.
In all of its appearances except one before the Jupiter 2 takes off, the panel above that colorful but strange "rocking ball" device - which purpose is never explained - is devoid of any display indicators; only when Dr. Smith's attention is drawn to it, showing the "ROBOT POWER" being disengaged, does the (redesigned) panel have a display. After the launch that display remains unchanged.
As Doctor Smith approaches the Robot in his attempt to verbally override its sabotage rampage ("Abort! Abort!"), Penny rotates 180 degrees.
An Alpha Control technician informs the president by "scrambler" phone that the Jupiter 2 "has passed the limits of our galaxy." Even at FTL speed that would not be possible that quickly given the length of time stated to reach Alpha Centauri. However, stating that the Jupiter 2 has left the limits of our solar system may have been a possibility.
The spacecraft is shown going through an asteroid field, with the rocks bouncing off the craft and flying away aft of the ship. Newtonian mechanics would have the rocks flying off in the direction they were redirected after the hit, not falling off to the rear of the ship. This indicates that the model of the ship was placed in a vertical mount and the rocks were dropped onto the model in a gravity field.
When the last 30 seconds are being counted down, it takes 9 seconds to get to 25, 18 more seconds to get to 20, 14 more seconds to get to 15, only 3 more seconds to get to 10, and then the last 10 seconds are counted a little slower than actuality.
During the "weightless" scene, the wires holding up Will and Penny can be seen.
When the Major and the Dr are checking the equipment and saying how cold it is. You can see they're visibly sweating.
During the Robot's sabotage rampage, its speech indicator (the translucent panel above its eyes which lights up when it talks) works normally on the lower deck, but never illuminates on the upper deck.
During John Robinson's spacewalk the wires holding him up are visible, against the white background of the nebula. Also, light reflects off one of the wires.
The narrator calls the Jupiter 2 an "intergalactic" vehicle. It plainly isn't, as the J2's stated mission is to travel from our star system to a neighboring one, within the same galaxy.
The Jupiter 2 instrument that shows speed/acceleration is labeled LINEAL ACCELERATION. The label should have read LINEAR; lineal refers to an ancestral line.