Winchester primers are prone to flattening. Might try some CCI, they have a harder shell.
I ran into this a few years ago as well, did damage to the bolt face of a Mauser I had. Contacted Winchester and they took back all the primers I had of that LOT # and replaced them. They were aware of the issue and fixed it.There is nothing wrong with flat primers. When they flow into the surrounding groove, you have a problem.
Winchester used to make high quality nickeled primers, up to about 10 years ago. Some batches of the non-nickeled were so soft that they allowed bypass, essentially putting divots in the faces of bolts. Folks that didn't catch it in time had a circle of divots in the bolt face. Not just M14 bolts, but those of bolt action rifles as well.
As I recall, TonyBen found out the hard way.
I swore off Winchester primers at that point. There are better options.