We had this issue for a little while when DS was 2.5/3 - and we ended up switching to gap and gymboree socks for now. They were softer than the generic brand (babiesrus?) brand and that made a difference for him. At home, we have the kids run barefoot. I also noticed that certain shoe brands made the issue worse for him (no more generic target shoes for us at least for now) - if my own experience is go by, it would have to do with how the seams line up with the stitching on the shoes (some sneakers, I really dislike because of that sock seam/shoe stitching rubbing on each other).
Now, he is careful about noting where the seam is on his foot.
