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.)
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.
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.