This sounds like something I've experienced on my commute bike which has disks and QR wheels.
I hadn't had to remove the rear wheel for some time but needed to replace the pads for the disk brakes. I then struggled to get the rear wheel positioned back into the frame without the pads rubbing on the rotor. Once I did manage this even after a short distance of riding (and braking) the rubbing returned (to the extent that the rear wheel would only spin a couple of times before it stopped). I realised that when I released the QR I was able to twist the wheel within the frame and close inspection of the dropout revealed the type of damage you describe. I've a photo of it but the wearing of the frame is not that clear.
It seemed to me that my QR wasn't holding the wheel in place tightly enough so having read some articles on internal and external cam QR I bought a Shimano Ultegra QR.
Bike Radar Quick release feature
Shimano Ultegra QR
The new QR was certainly an improvement on the old one and seems to clamp better. I still had to readjust a few times but now it seems that the rotor rubbing has stopped (or it's just worn the pads down to accommodate - hoping not though!) and that the wheel is secure in place.
I did also buy some metal putty and made a half hearted attempt to place some putty just on the edge of the frame where it was worn in the direction of the axle movement but it didn't stay put. I think to do it properly you need to use plenty of putty so there is enough to adhere to the frame with some strength. I think you'd have to be careful on getting putty on the clamping face though.
Metal Repair Putty
I've not had this problem before on bikes with rim brakes and wonder if it's caused by a mixture of insufficient clamping, whether that being the QR not being tightened correctly or the serrations on cheap QRs not gripping the frame enough, and the fact on a disk braked bike the braking force is on one side of the wheel only - leading to a twisting effect.
My only other disk brake bike has thru axles which I'm pleased about - not sure whether this was one of the reasons for thru axle development but I'm hoping it's solved this particular issue.
It would be interesting to know whether you have the same disk brake/QR set up.