well there are issues everywhere... begin by reading the posts about the flood here: http://corior.blogspot.com/ (especially the parts about the gilgamesh epic) and then http://www.talkorigins.org/faqs/faq-noahs-ark.html (also read talkorigins 29 proofs for macroevolution while your at it).
Since it seem that faith has nothing to do about proof you might as well have a bit of fun, so you could ask who on the ark had syphilis, polio, gonorreah and a gazillion other diseases that only humans can have. it raise the interesting question how the worlds 8 most virtous people would carry multiple sexual diseases. And when you factor in that some of these have a limited lifespan so they would have to jump around different members of the crew things become interesting... this, ofcourse, also hold for the other animals. Bird flue in a giant floating bird-cage without the option to isolate sick birds, what fun!
The only answer i have got is that "they originated spontaniously". Oh, so its impossible that life arose over a billion years on earth, but a range of fully functioning modern vira can spring into existance in a mere thousand years or so? its difficult to answer that without contradicting yourself (sometimes you get the automatic response that they could have caught the diseases from corpses. forgetting the fact that few if any diseases survive in a year-dead corpse, it does raise the question of what vector will give you a STD from a corpse! ;-)
It seem that most jws trust the water canopy theory and use it for a lot, like how the water came to earth and why carbon 14 is misleading. Here is a fun calculation you might walk someone through (only requires highschool math and physics):
The idea with the water canopy theory is that a large quantity of water is around the earth and block out radiation from space in such a way that AllIllogicalThingsWork(TM). the average show of spongebobsquarepants is more physically sound than this, but nevermind that for a moment.
First is the question of how the water is held up. The idea that the water is held up as vapour in the air is abselutely redicilous (which i think every jw willl agree with) since in terms of atmosphearic preassure, it does not matter if you walk around on the bottom of a 1km deep ocean, or on the bottom of a 1km ocean with a little air mixed into it (which is the case if the water was suspended as vapour). The pressure is the same, and if a human has to just dive to 200 meters depth it takes a lot of special equipment since normal air is toxic at that depth and will generally ruin your day. besides, to keep all of that water as vapour, you have to keep it very hot. think hundreds of degree celcius.
So even proponents of the water canopy theory will see that having everybody at noahs day being boiled and suffocated at the same time as a bad thing, and what is proposed instead is that the water is actually in orbit around the earth as ice. This is certainly possible (allthough it would orbit earth a a belt like the rings of saturn, not actually doing much good in terms of blocking out the sun, but nevermind), however there are still certain problems.
The grand moral of physics seems to be that God is kind of a cheapass in terms of energy. Energy cannot be created from nothing, energy cannot be removed. It seems that however god designed this universe, it was paramont of him to preserve energy, and finding an experiment where energy is not concerved is something that would give you the nobel prize in no time. What does that have to do with the ark? Well, highscool physics teach that it takes an energy E to move a block with mass m a height h up into the air where
E = m h g (g being the gravitational constant, which is approximately 10 m/s^2
Now, if that block was to fall down again, the energy would have to go somewhere (remember that god is a cheapskate) and unless one construct a device to store it it will be converted to heat. This is what happends when a spacecraft lands on earth: Because its a great hight above earth it has a lot of energy, and that energy has to go somewhere. The great bulk of it actually goes into the atmosfeare, and it become so hot that it litterally glows around the spacecraft. Now back to the water - lets try to put this into context. The energy required to raise the temperature of water one degree kelvin (or celcius) is about 4000 joules per kilogram. How high up would the canopy have to be? Lets just say 400 km for argument sake - this is really a minimum, since the atmosfeare extends quite high above the earth and cause a drag, which in turn slows down things in orbit and cause them to crash down.
Now, lets say that 1 kg water falls from a height of 400 km. It would aquire an energy of
E = 1 * 400*1000 * 10 = 4*000*000 (joule).
If all that energy went into the water, it would raise the temperature of it to 1000 degree celcius. Water boils at 100.wood burns at 300.
So if one were to deorbit the entire atlantic ocean, it would be superheated. The atmosfeare wont be of much use - air is a pretty poor medium for storing energy so it, to, would be scorching warm. There is simply no physically sound way to fix this - you either require a miracle (and in that case, every theory, no matter how bonkers it is, can be supported) or accept that earth got the big trip to a disinfection station. And saying that "some of the water came from the earth" is a pretty poor way to fix it, since you dont have to go far down in the earth to find really high temperatures to (there is no such thing as a cold geyser).
* Gravity is not uniform but degrees the further you come from the center of the earth. The relationship is 1/r^2, so with 400km thats about 11% the calculations are off on that count, and to get better results one should also factor in the kinetic energy (Which would increase the temparature) and that the specific heat of water depends on temperature and other stuff. this does not change the conclusion.