Could it also be that the sole of the boot on the other foot grazes this spot once in a while? Unless you're wearing stiff denim, I can't understand how the pants could do that.
A couple of fixes come to mind. Find some tall socks to wear, either hiking socks, or a thin liner sock that goes calf-high. Or before the hike, wrap one or two rounds of tape around the leg where the sore appears.
