Althought our female common ancestor lived about 60,000 years ago, that does
not mean that there was only one human female alive at that time. All that it means is that we all are descended from that one female
and others.
We could not have descended from one single couple because we are too genetically diverse. We have observed that species consisting of only a few individuals or species descended from a few individuals have very little genetic diversity and tend to go extinct. Genetic diversity does increase over time, due to mutations and what-not, but we have measured its approximate rate. The rate is far, far too slow to have generated the observed human genetic diversity in anything less than a few millions of years.
Since we have these measures of genetic diversity, we can detect species that have descended from a few individuals; in other words, "passed through a genetic bottleneck". In species that have passed thorugh a genetic bottleneck, we can derive the approximate time when this happened. If there was a Noachian flood,
all species should have passed through a genetic bottleneck at the same time. But they didn't all pass through a genetic bottleneck, and those that did, did so at different times.