The VBUS pin was designed to tolerate a maximum voltage of 5.25V in accordance to the USB 2.0 Specification. When this voltage is exceeded (we’ve seen this to happen at about 5.6V) the current that flows into the internal protection diode increases causing a breakdown which then destroys the internal VBUS trace, rendering the USB controller non-operational. This condition is irreversible.
A 1 Kilo Ohm series resistor can be placed closest to the VBUS pin, as shown in the circuit below, to limit the current that flows into VBUS once the diode voltage breakdown has occurred. This will prevent damage to the VBUS pin.
Another solution is to use an over-voltage protection chip. A quick search returned this part, NCP362, by ON SEMICONDUCTOR (I’m sure there are others out there):