I had a 160mm disc rotor on a road bike that was rubbing a bit in one spot, not severely, but enough for me to notice. I've tried to true it a few times over the past couple months with little improvement. I finally ordered a new rotor (sram centerline) and noticed it's also touching the pad, possibly more so than the old, but it sounds better under hard braking oddly enough. I checked the new rotor before I put it on and it was straight. I'm wondering if my hub is just imperfect and that's whats causing the alignment issue. Is this common and if so is there a fix?
It could be a number of issues but I doubt you got a bad hub. Check to make sure your wheel is seated correctly in the fork. You could also try tightening/loosening the skewer to see if that may help align things. If all that doesn't work then you can try to realign the caliper if necessary. I wouldn't worry much if its just a little rub.
I think @itsthejash has some good tips but I'd also suggest taking the rotor off the hub and making sure there is no dirt or other material on part of the mounting surface of the hub, thus pushing it out in one spot. Maybe use some cleaner to ensure the surface of the hub and rotor are clean on the faces that meet during mounting.
Also - when you engage the QR, I find it useful to be putting some pressure down onto that axel to make sure it is perfectly seated - although it sounds like your problem is pretty consistent so I don't think this will fix it for you.
Have you tried adjusting it at the caliper ,just dial it back a notch or maybe two ,but make sure your brakes are still effective when you do.
Some ideas - mark the rotor where it rubs. then remove and refit the rotor but turn it 90 degrees relative to the hub. Does it rub in the same place or 90 degrees away? I think you'll find the lump follows the hub, not the rotor.
Use a straight edge (like a steel ruler) across the flat of the rotor mount to look for any imperfections - they will be really small. If nothing is visible, use a dry-erase marker and colour the whole surface in, then scrape your straight edge over it. There may be bits which scrape clean and bits that don't. The high spots will be scraped clear and the lower spots will remain coloured.
Refit the wheel to the bike, with no rotor. Spin the wheel by hand, and use your eye or by touch to detect if the hub/rotor mating surface varies at all. You may need to use a straight-edge to see it better.
If you find a slight machining error, you want an engineering company to mill it flat. A company that does engine head work should have the right gear. Don't try this with hand tools!
If thats not possible, replace the hub and rebuild the wheel, or replace the entire wheel, or simply put up with the scrape.