If Noah brought two of every animal that was worth having along, they probably came with all sorts of parasites. Noah himself probably had a few. Unless you claim he only brought along two of each, including the asexual ones, I don't see why that would be a problem for the idea of a global flood. Not that it doesn't have a million problems already, but parasites, surprisingly enough, don't add one more that I can think of.
Now with earthworms, I think a lot of people in this thread were considering them as being left out. I don't see why Noah couldn't have just taken a bucket of dirt and worms aboard with him and kept them alive for the duration of the flood. It would be much easier to ensure the survival of earthworms than it would be for, say, penguins, or elephants, or any of the countless species of large, dangerous animals, like hippopotamus or grizzly bears.