Sulu reports that the planet killer is pursuing the Enterprise. The next shot is an exterior one, showing the Enterprise with nothing in pursuit.
After the planet killer attacks the Enterprise, Spock and Decker race to the helm to level the ship. A wide shot shows McCoy and the two security guards in the background getting up. Then, after the ship is stabilized, there is a close up shot of Spock and Decker, with McCoy and the two security guards getting up again.
When Commodore Decker's shuttle leaves the bay, the star field in the background changes mid-scene.
When Mr. Scott beams over to the Constellation, he wears a kit of some kind that is held by a diagonal strap over his right shoulder. The strap is visible just before the Constellation gets underway, but after the ship starts to move, Scott is not wearing the strap as he is thrown off balance and clings to machinery and the hexagonal grid behind him. Then the ship's ride smooths out, and after a cutaway to Captain Kirk, Scott is suddenly wearing the strap over his shoulder again.
Kirk gives Spock instructions on the procedure to activate the transporter within a thirty-second window, and then places his communicator on the comm panel. In the next shot, he's holding the communicator again.
The three men who accompanied Scott on to the Constellation should have been wearing red uniform shirts. A damage control party would consist of personnel from Engineering, not Command or Life Sciences.
When Sulu reports that the planet killer is closing on "Enterprise", Decker orders "Maintain speed and distance". If the machine was gaining on them, it would be necessary to INCREASE speed to maintain the same distance from it. However, Decker is not completely compos mentis.
When the Enterprise shields are depleted, the planet-killer hits the Enterprise two more times. Assuming the planet-killer used the antiproton force-beam it used to break up the planets, the Enterprise should have been completely consumed in a massive antimatter explosion. However, the Enterprise also has deflectors, not as powerful as the shields but certainly of some use.
In attempting to steal a shuttlecraft from Enterprise, it would not be possible for Commodore Decker to de-pressurize the shuttle hangar deck or open the shuttle bay doors from within the shuttle craft, however, many other characters throughout Star Trek history have done just that, and therefore it is possible. Further, as soon as the hangar deck began depressurizing, that should have become known to someone on the bridge via an alarm, most likely at Mr. Scott's engineering station, in plenty of time to reverse the process and 'lock the doors'. However, it is a common plot device throughout The Original Series as well as the spinoffs for a shuttlecraft to be stolen before the crew can react to stop it. Therefore, it should not have been known quickly enough to Mr. Scott or anybody else, according to Star Trek canon.
The scale of the planet killer device compared to the Enterprise and her shuttlecraft varies. This discrepancy was later partially corrected in new visual effects in the remastered 40th anniversary edition. However, a new mistake is introduced in the remastered version: the scale of the shuttlecraft in relation to the Enterprise is far too large. If the shuttlecraft were truly that big, then the Enterprise herself would have trouble fitting even 40 people inside the hull, much less the full crew complement of 435.
After the planet destroyer wipes out the Enterprise's shields, Lieutenant Palmer gives Spock a damage report before the machine attacks again. Elizabeth Rogers, the actress playing Palmer, anticipates the "attack"; she begins to collapse toward her chair a split-second before the Enterprise is "hit".
Obvious stunt double for Commodore Decker when he rebels on the way to sick bay. However, this would not have been "obvious" on the small, low-resolution TV screens of the 1960s.
The background star field can sometimes be seen through certain light color parts of the planet killer model.
Boot scuff marks can be seen on the floor of the corridor before Decker fights the guard, showing that there had been practice or prior takes of the fight. Also, at the end as Decker drags the guard out of the hall into the room, the floor seams appear to be uneven, as if they were coming apart - probably caused during the fight.
The syndicated version cuts out the part where Scott tells Kirk that he's hooked in the Constellation's communications system. Cutting this out takes care of a problem, which is why Scott would be wasting time fixing the ship's communications system when their hand held communicators were working just fine.
On the Constellation, Scott tells Kirk that they can replay the duplicate captain's logs from the auxiliary control room. Kirk is the first to arrive there, but he almost walks past the room, the same room they were heading to.
Early in the scene where the landing party first finds Decker, there's a brief cutaway angle to Dr. McCoy that was picked up from footage used a few minutes later, but optically flopped to match his position (screen left) beside Decker, made evident by MCoy's hair being combed to the left instead of to the right.
When transporter chief Kyle first reports to the bridge that the transporter is out, his voice is heard as if it's on the bridge and not through the intercom.
As the Enterprise (under Decker's command) is being drawn into the planet killer, the actors on the bridge can be seen reacting to a "whining sound" that was specified in the script, but ultimately not used.
When Decker and Montgomery are engaged in hand-to-hand combat, an audio "Bam" can clearly be heard when one of the punches lands.
Just before the transporter failure during the attempt to beam Kirk back to the Enterprise, the gray/white flash powder is visible on the leftmost transporter pad, around the 1 o'clock position.
When the Enterprise is attacked, the transporter is disabled. Kirk and the away team are stranded on the Constellation. Right after Kirk tells Washburn where to go so they can try to get the view screen working, there is a brief shot of the shadow of a boom mic at the left side of the screen.
Decker is clearly unfit for command when he takes the Enterprise. When McCoy first finds him, he's in a state of extreme shock and borderline catatonic, and even after McCoy gives him a shot to bring him out of it, he slips in and out of complete hysteria. McCoy would easily be able to prove this should Starfleet make an issue of it, particularly since as CMO, he has the authority to order a physical or psychological examination of any crewman serving on the Enterprise (as Decker now is) at his discretion.
For reasons unknown, this episode ignores the Enterprise's secondary weaponry, the photon torpedoes.
Possible tactical goof: Once it became apparent that phaser fire could not penetrate the neutronium hull of the Planet Killer, why did neither Constellation (before the episode even started) nor Enterprise attempt to fire phasers or, better, photon torpedoes 'down the throat' of the machine?
As Scotty leaves the Auxiliary Control Room for Engineering, he says to Washburn, "Come along, lad." As Scotty walk off camera, Kirk immediately instructs Washburn to "get in there", countermanding Scotty's order.
It is beyond even the science fiction logic of Star Trek that the 'planet-killer' robot would have originated from another galaxy, as postulated by Spock. As established in the story, the device replenishes its energy "digesting" chunks of the planetary bodies it destroys. During its millennia-long traverse of inter-galactic space, it would encounter no sources of fuel to sustain its systems, and would thus arrive in the Milky Way galaxy a 'dead' machine artifact.
When Scott tells Kirk how to set the controls to detonate the Constellation, his Scottish accent vanishes when he delivers the line ""Press this one... 30 seconds later, poof!" His subsequent lines display the correct accent, however.
When Kirk tells Spock to beam Scotty back to the Enterprise, how does the transporter chief know which one of the two humans is Scotty? He didn't hear the call, so he doesn't know who has their communicator open and active.
When Washburn tells Kirk to try activating the Constellation's view screen, before Kirk can see anything but static, he says "What the hell is going on?", as if to say "Why is the Enterprise attacking the Doomsday machine?"