Jamieson, Fausset and Brown on Numbers 31:7

7. they slew all the males--This was in accordance with a divine order in all such cases (De 20:13). But the destruction appears to have been only partial--limited to those who were in the neighborhood of the Hebrew camp and who had been accomplices in the villainous plot of Baal-peor (Nu 25:1-3), while a large portion of the Midianites were absent on their pastoral wanderings or had saved themselves by flight. (Compare Jud 6:1).