Why do people think there is some necessity or advantage of using a Schottky diode for this purpose?
If the diode is across the fan terminals and there is significant length of cabling between the diode + fan and driver, the spike may be due to inductance in the cables. All the more so if you happen to have included interference suppression inductors in the lines.
If you want to protect the driver from spikes, it makes sense that the "kickback" diode is fitted in the driver board itself. Don't forget to check the waveform on the supply rails also.