Mega2560 has 2 Crystal Oscillator?
There are two devices on an Arduino board than need a clock source:


The ATMega328 / ATMega2560 main MCU (16MHz)
The USB interface.


The USB interface crystal speed depends on what device is used on your board. Genuine Arduino boards use an ATMega16U2 which uses a 16MHz crystal.  Cheap Chinese clones use a CH340G which takes a 12MHz crystal.

Note that normally it's one crystal and one ceramic resonator.  USB requires very precise timing, so a crystal is used for that. The main MCU doesn't need quite such precise timing, so a cheaper (and less accurate) ceramic resonator is used.