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