Plot hole: Even if the white blood cells will attack and destroy the sub and the body of Doctor Martin 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.

Fantastic Voyage (1966)
3 plot holes
Directed by: Richard Fleischer
Starring: Donald Pleasence, Edmond O'Brien, Raquel Welch, Stephen Boyd
Revealing mistake: It's painfully apparent that the actors are hung on wires pretending to swim while outside the sub.
Wireless Operator: A test message from the Proteus, sir. Miss Peterson has smiled.
Col. Donald Reid: Well, that's an auspicious sign.
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