I checked the ammo box theory, but the lines don't match up. I felt all the cases with a sharpened and bent paperclip, did not noticed anything with that method. I have no idea, I will load a few of them and see if it gets worse or more noticeable on the next firing.
I will also look into the shoulder bumping thing. I figured I'd always full length size to keep things simple, but I can see why you don't always want to be doing that.
There is nothing wrong in that picture. That is a perfectly normal thing, that's just how your sizer hits the brass. Do not worry about it.
There's lots of opinions on sizing brass, and even more methods on how to get there. Full length sizing every time is a perfectly acceptable method of doing it, and by far the most common. What Wapitibob is saying is that brass doesn't always form completely to your chamber. If it did, you wouldn't be able to extract it. By firing 2 times without body sizing you are expanding that case body closer to your chamber size. You can run into issues with this method though, one being you might not be able to chamber your rounds. This depends on your brass, how hot your loads were, etc.
If you measure a handful of cases for headspace (being sure the primer isn't effecting your reading), you will find they will vary in that base to datum measurement. This is normal, and happens from variation in brass spring back. What I do is use a number on the higher end, and use that for my reference. I will then normally size to bump that shoulder back .002" to .003" ideally. Many shoot for less, but this is the range that works for me. If you are shooting for that minimal .001" bump, you will probably find you need to anneal your cases. The variation in your brass hardness will make it very hard to keep your headspace variation case to case that low without annealing. Even with annealing it can be tough to do, and sometimes impossible with normal expander ball full length sizing dies. That expander ball pulling through can wreak havoc on your headspace consistency, as well as neck concentricity. A lot of people go to bushing sizer dies for this reason. I do a 2 step body sizing, then neck sizing process.
That's a lot of info to throw at you. If you don't anneal, and use a normal expander ball full length sizing die, my advice is to check your measurement, but you are probably fine. I've never seen a .010" bump from setting a die by instructions as has been said. Even cheap Lee dies if screwed all the way to the shell holder only bump the shoulder .004"-.006" on every caliber I've tried it on. That's how I used to load all my ammo. It isn't ideal, but it isn't that bad either.