External display : why 59Hz instead of 60Hz on Macbook Pro 15" mid-2012 @ 2560 x 1440 via DisplayPort
You can pretty much always attribute this one to a rounding error in the way the information is displayed to you. The actual refresh rate is somewhere very near 59.97Hz, leading whatever function they've run the number through for parsing to only display the whole number digits, and not perform any actual rounding.

This does lead to some interesting effects though. Some applications will do this and end up with a V-Sync rate that's not actually synced (They fake it and do framerate lock instead, leading to 59fps when you actually need 59.97fps exactly.)