Nonsense of Noah
Fruitflies represent just one of nine hundred thousand problems with the insect world. Every insect presents some kind of problem to the idea that the Ark had "of every creeping thing of the earth after his kind, two of every sort...
Many species, including fruit flies, have very short lives, and the original pair would not have survived the trip to the Ark or on the Ark, making it necessary for reproduction while on the ark in order for the species to survive. A fruit fly is sexually active within 5 hours of hatching. Their generation times are very short. By the end of the 40 days and 40 nights (not to mention the time waiting for the waters to recede), the ark would have been filled from one end to the other with annoying fruit flies.
This assumes of course that Noah was able to find, transport and keep fresh, enough fruit for the pesky fruitfly.
Again, this little problem is just representative of the nature of the problem with all the insects on board.