Plot hole: When a crew member of the miniaturised submarine is eaten by the blood cells, the fact that his atoms will return to full size at the same time as the rest of the crew and the submarine (which provides the suspense, such as it is) is completely ignored.

Factual error: 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 for the laser gun which they forgot or left behind on purpose.

Revealing: 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.)

Other: During the miniaturizing scene the technicians controlling the forklift wore sterile gloves, the nurses assembling the syringe did not.

Revealing: 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.