One example, which I believe is fairly well known, is that various species of cicadas reproduce at periods of prime numbers (e.g., $13$ and $17$ for $2$ specific species) of years. As for the reasons for this, it's not completely known or understood, but Wikipedia's Predator satiation survival strategy section of their "Periodical cicadas" article says:
The emergence period of large prime numbers (13 and 17 years) was hypothesized to be a predator avoidance strategy adopted to eliminate the possibility of potential predators receiving periodic population boosts by synchronizing their own generations to divisors of the cicada emergence period.[16] Another viewpoint holds that the prime-numbered developmental times represent an adaptation to prevent hybridization between broods with different cycles during a period of heavy selection pressure brought on by isolated and lowered populations during Pleistocene glacial stadia, and that predator satiation is a short-term maintenance strategy.
Another example is how the Fibonacci numbers occur in nature in various ways. The Science article at How are Fibonacci numbers expressed in nature? explains various cases in some detail, especially on the second page, including how this also applies to honey bees.