The animals were only on the ark 190 days (40 for the flood, 150 while the waters receded). While it is true that for many smaller animals, that is within their gestational period, for many of the larger ones it is not. As such, the total biomass isn't going to be affected that much.
Additionally, while the exponential power of generations can be formidable, it takes time Take rabbits, for example. According to this article on rabbit breeding, the average rabbit has a gestational period of 28 - 31 days, and can begin to reproduce at 6 months. That means even if a rabbit got pregnant on the first night in the ark, her first litter would only be able to reproduce in the last week before getting off. According to the same source, if a rabbit produces 20 offspring in a year, that's a good ratio. (And, good eating, but I digress).
Admittedly, fruit flies reproduce in days, but they also die in a week, and even a whole lot of flies isn't a lot of biomass. Even one litter of elephants, by contrast, would have been quite a deal- but they take 22 months to gestate, and thus would have been off the ark by time they were ready to give birth.
All this is to make one simple point, due to the amount of time on the ark, things may not have been great, but it wouldn't have been a total zoo. (Rim shot)