Why are there 3 crystals on the Mega2560 schematic?
One of the crystals is for the ATMega8U2 chip which is being used for USB-Serial conversion.

The other two crystals are both for the ATMega2560. Why two? Basically they only populate one of the two, but they have two different footprints. One is for a surface mount resonator, the other for a through-hole crystal. 

Having two footprints gives the option during assembly to go for the cheapest package at the time. It also means that the hobbyist can replaces the low accuracy resonator with a high accuracy crystal if their project requires. 



As a side note, if you look at Y1, you will notice it is not the symbol for a crystal, it is of a resonator.