When M5 begins the attack on the Federation task force, it concentrates most of its attention on two ships, the Lexington and the Excalibur, with a single attack on a third ship, the Potemkin. The fourth ship of the task force, the Hood, is never attacked by the M5-controlled Enterprise. However, when Commodore Wesley contacts Starfleet and asks for permission to destroy the Enterprise, he states that all four ships have sustained damage.
When Lieutenant Uhura informs Captain Kirk that the M5 had already acknowledged a transmission from Commodore Wesley, her left hand is holding the earpiece in her left ear. As the camera cuts to Kirk for his reaction, her hand is at her side.
When the Enterprise is attacking the other four Star Ships, Uhura is saying she cant communicate to the other ships, but Kirk should've used a hand held communicator to contact other ships to say what is going on.
Commodore Wesley knows that the M-5 is intended to take total control of a starship, and the wargame was an experiment intended to prove that it actually worked as promised. However, when the Enterprise acts erratically and makes lethal attacks on the attacking force, Wesley demands to know what Kirk is doing, with no indication that he considers the M-5 to be responsible. But Wesley does not know that M-5 has made it impossible to disconnect it. Thus, Wesley's concerns are made on the assumption that Kirk can and should order M-5 turned off.
As the Enterprise approaches the space station, Kirk orders "standard orbit". It is impossible to orbit a space station since it wouldn't have enough mass unless it was the size of a large moon or small planet. And there is no nearby planet shown for the ship to orbit.
It is possible to orbit (i.e., move in a curved path around a large object in space) a space, although it would require motors or thrusters, rather than merely momentum while under the influence of a gravitational field.
(Digitally remastered version) Wesley reports "all ships damaged", yet, when the three surviving starships prepare to attack the Enterprise, there is no sign of damage to any of them.
The entire M-5 project should be going forward under the tightest security. All information on the project should be on a strictly 'need to know' basis. Spock should know about Richard Daystrom's previous work, but since he has not been involved in the M-5 project, he should know nothing about it as the episode begins.
As Kirk, Spock and McCoy ride the turbolift to engineering, Spock observes that it is unfortunate that no computer can replace a starship surgeon. As they exit the turbolift, McCoy replies "Very funny" but his mouth is not moving.
After Kirk, Spock, and McCoy exit the turbolift to Engineering, McCoy says "If it could, they wouldn't have to replace me, I'd resign..." McCoy's lips do not match "If it could".
Daystrom claims he want M-5 to supplant all human space exploration. But after analyzing the planet in the first test scenario, M-5 still requires an experienced crew and a science officer to make the actual examination of the planet.
McCoy notes that having a crew of only 20 aboard is insufficient to properly operate the ship if the M-5 fails. From a safety standpoint, no experimental equipment would ever be tested without reasonable safety measures in place to handle a catastrophic failure, including having a sufficient number of personnel on hand to handle an incident.
For unknown reasons, the M5 attacks and destroys an unmanned ore freighter. While Kirk and McCoy both demand that Daystrom offer an explanation. At no time does anyone think of directly asking the M5 why it took such action.
Photon torpedoes must be manually loaded into their launchers. M-5 would not have been able to fire them. Additionally, it is established in Mirror, Mirror (1967) that the phaser banks can be sabotaged. Why didn't Scotty suggest it? Or beaming M-5 out into space, as in Wolf in the Fold (1967)?
As M-5 is evaluating a planet for exploration, Scott remarks that M-5 is cutting off power on decks 4 and 5. In the following scene, Dr. Daystrom explains why power was cut off on decks 4 and 6. Captain Kirk's quarters are on deck 5, which should still be available as he remains on the ship.
When the crew has regained control of the ship and Federation forces are about to attack the Enterprise, Captain Kirk asks for "inter-ship communication" (verified with closed captioning). However, what he is expecting, and gets, is intra-ship communication, as communication with the other ships is impossible, as required by the story line. They can't explain to the attacking ships what has happened.
After attempting to disrupt the M-5 and take over manual control of the helm, when Sulu calls back to tell Kirk he does not have control, Kirk responds with "Kirk here" before pressing the intercom button.