Scientific mistakes
If the submarine´s crew had been shrunked on atomic level, they wouldn´t be able to breathe the air out of the lungs of the body they are in. The oxygen atoms would be too big to connect with the hemoglobyn of the shrunked red blood cells.
Same thing is in "Innerspace", when Dennis Quaide is adviced to bring new air in his capsule from the lungs and when he drinks whiskey out of Martin Shorts gullet: What he get there is, in his dimensions, no real whiskey, because its atoms would be much bigger and the ingredients more separated.
And I also think, that there are mistakes in the scale: If the submarine is the thousandth of a millimeter long, the needle of the syringe and the various parts of the body would had to be much bigger for it.
"Hooters, hooters, yum yum yum,
Hooters, hooters, on a girl that´s dumb!"
The Bundy credo