are you talking about the Stepper Motor Driver v1.1? [
parts.reprap.org]
this is actually the right behavior... if you look below the part list, it has the human readable list (including the math... which will explain it.)
for example, the .100" breakaway headers come as a pack of 40, but you only need 18 total for all 3 boards:
571-41032390 (buy) .100 breakaway header 18 needed / 40 per unit 1 total