The main reason for the small noise in stepper motors is higher harmonic resonance that they are driven with. Stepper motors are driven by square wave current, which must contain a large number of higher harmonics, thus sometimes producing vibration and noise.
On the 200mm Coil Winder we use Closed Loop Motors. With the Closed Loop motors also you will sometimes hear a slight squealing while standing still and this is due to the built in encoder always monitoring where the shaft is and correcting itself. You will notice if you try to turn the motors they will self correct back to the position they were in before and also you will hear the noise change when doing this.