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.
Revealing mistake: It's painfully apparent that the actors are hung on wires pretending to swim while outside the sub.
Factual error: Proteus refills its air supply in the lungs. The lungs are filled with normal sized oxygen molecules. How are they supposed to breathe them? (In the book, they had a miniaturizer on the sub, but there is nothing in the movie to explain this.)
Revealing mistake: During the miniaturization process after Phase I, the sub has been reduced to coin-size at best. As the techs are beginning Phase II, they roll wheeled equipment by the tiny sub. There is a close-up of the sub pilot looking eye-level with the equipment wheel axle, and a tech's ankle is slightly below the pilot's eye-level. This is an impossible perspective: for the pilot to be eye-level with the wheel axle, the sub would have to be more like a foot in diameter and not coin-size. (00:27:10)
Factual error: During the whole voyage except when getting very close to the heart there is no pulse seen either in the blood or acting on the vessel.
Revealing mistake: Near the beginning of the movie, Grant is in the car being lowered but the shadow the car makes remains the same.
Revealing mistake: Near the beginning, when the car is lowered into the underground complex, the car is sitting on a section of the street pavement above. When shown underground, it's sitting on a rug or carpet that appears as if it were supposed to represent a dirt surface. There are even visible tire tracks. (00:07:20)
Factual error: Where is all the light coming from inside the body?
Answer: I think the countdown began after the crew were injected into the patient's body.
No, the countdown started after the second shrink.