Plot hole: Even if the white blood cells will attack and destroy the sub and the body of Doctor Michaels the atoms would still remain and take normal size after the critical 1 hour is up. This would also apply to the laser gun which they forgot or left behind on purpose, as well as several dozen litres of saline solution which were miniaturised and pumped into Benes' body. He's in a lot of trouble.
Other mistake: During the miniaturizing scene the technicians controlling the forklift wore sterile gloves, the nurses assembling the syringe did not.
Wireless Operator: A test message from the Proteus, sir. Miss Peterson has smiled.
Col. Donald Reid: Well, that's an auspicious sign.
Question: Just an observation. There's 5 or 6 minutes of screen time between the initial shrinking of the sub / crew and the start of the 60-minute clock. Shouldn't those minutes have been included in the countdown?
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