When your microcontroller comes up, it's GPIO is in high-Z state, maybe pulled up(that means there is an internal resistor to VCC which may be enough to turn on the LED) . Its a good practice to pull down anything you don't want to work uncontrolled. So when the firmwarenwill initializefirmware initializes the outputs, you don't need the pulmpull down resistors anymore. Only onpoweron power up/down or JTAG programming.