Plot hole: When Captain Kirk is the last person unaffected by the spores, he's on the bridge lamenting the fact that he is trapped in orbit above the planet since he can't pilot the ship alone. He also can't call for help because Lt. Uhura sabotaged long range communications. but Captain Kirk has somehow forgotten about the shuttle craft. He could have easily escaped on one of those.
Continuity mistake: As Kirk sits on the deserted bridge, there is nothing out of the ordinary with him. After he sits at the helm position, the camera looks at him over the console, and there's suddenly a spore spewing plant to shoot him.
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