reading the data sheet for the nrf I found the following statement “When VBUS rises into its valid range while the device is in System OFF, the device resets and transitions to System ON mode”.
Looking at the schematic the Vbus pin is directly connected to the vbus of both the usb and the nrf, so this will always wake the device (And feed back into the PC!) which begs to wonder why this was used instead of connecting it the vin side of the lipo charger after the protection diode. So to me looks like a hardware defect.