Some of the pins are 5V tolerant, but some are not. Please see Zach's post here for more info:
If you use the Vin pin for power, you may starve the Core of it's stable power supply if for instance you draw too much power with servos, high power LEDs or other heavy loads. This could cause the Core to brown out and reset. If that happens you could always try to use a beefier power source, such as a 5V 1A or 2A wall adapter, or separate battery power supply between 3.6V and 6V on Vin.