I thought through-axles would help eliminate this kind of thing. I have conventional quick-releases, and this is a frequent occurrence. There seems to be quite a bit of potential slop when using drop-outs. The only suggestion I have is to use a torque-wrench and make sure you get the same (preferably recommended) torque setting each time you put the wheel on.
If it really bugs you, push the pistons all the way back into the calipers before mounting a wheel, and let them reset to the rotor after a few squeezes. If you make sure the slot of the caliper itself is centered on the rotor, I find it makes it more reproducible.