They have only a limited amount of time to get in, fix the problem, and get out before the effects of the shrink ray wear off and they spontaneously grow back to normal size. According to the scientists, objects stay miniaturized for only a
short time, depending on how much miniaturization the object undergoes...
But eventually the saboteur is caught, the blood clot is cleared, the ship is destroyed by a white blood cell and the crew escape Benes' body through a tear duct with literally seconds to spare before they end up back at full size. Phew!
But What About ...
Uh ... the wrecked submarine is still inside the patient.
OK, so maybe you're saying that for some reason not given in the film, the shrunken submarine was made from some special material that means it won't blow back up to full size when everything else does. Fine.
They also left Dr. Michaels behind. You know, the bad guy saboteur?
At some point he is going to return to adult size, from within the patient, possibly wearing him like a character costume at Disneyland.
Either way, it seems almost certain that the film should have ended with a bunch of embarrassed-looking and blood-spattered doctors standing around in an operating theater that looks like the final scene from a
Saw sequel, gazing at one another sheepishly and swearing a pact never to mention the whole affair again.