What he means (I think) was that you didn't take care to set the axle properly in the bottoms of the dropouts before tightening the QR. This is easier to get right with the bike upside-down and harder with the bike upright unless you take care to ensure the wheel isn't cock-eyed as you tighten the QR.
If doing the QR up really tight is forcing the wheel out of alignment, it's possible that a dropout is mis-aligned, which a decent bike mechanic ought to be able to sort for the price of a packet of biscuits and a polite "please", especially if you buy other goods from his shop from time to time.
Even more likely though is that the brakes have got moved over (road bike) and just need re-centring, or one of the pull-off springs is weaker on one side and needs tensioning with the little screw on the brake arm (MTB).