If the fan has 3 wires, the 3rd wire determines the speed of the fan, as measured and controlled by the motherboard.
At power-on, if the fan does not "feedback" the correct speed, then you see the warning that you have reported.
Later, if the fan runs at 100%, ignoring the motherboard's command to spin more slowly, then you will hear the extra noise from the fan.
For either reason, I would replace the fan.