I kept being unable to shut off the science part of my brain, the two things of: Marco's antibodies would kill them fast and at that size, just like in the first Helmacron book, they'd be unable to breathe-the oxygen molecules would be too big to get into their lungs and cells.
I like the Fantastic Voyage aspect overall, that was a good classic sci-fi movie. But I agree it's a little more childish when you're an adult. (I had this same issue with at least one Buffy ep, the reanimated dead kid-Frankenstein ep.)