Other mistake: When Chapel comes into Sickbay and looks at the "dead" Captain, the camera goes to close up of Kirk, and he wakes up. After she yells for McCoy, the camera goes back to Kirk, and he goes back to sleep. The motions of him waking are obviously played in a slow reverse instead of him quickly closing his eyes.
Plot hole: In the conference room, Spock informs Kirk that his theory of a Romulan cloaking device kept the sensors from detecting the ships. However, in S1:E14, "Balance of Terror", they figured out the cloaking device, and how it worked. Unless he was feeding into the deception, Spock shouldn't have had any theory when it was a fact.
Audio problem: During the scene where Kirk is talking in the briefing room, the director was obviously not pleased with how James Doohan said his lines. Due to budget constraints, instead of re shooting the scene, they simply replaced Mr Scotts dialogue with another one. You can see it since at one point his lips are completely out of sync, even on the remastered edition. (00:06:40)