Most of my flats I can associate with holes in the bottom of the tube and thorns, bits of metal or glass, etc., embedded in the tire or liner.

Sometimes I find small holes in the side of a tube, 90 degrees from the bottom, usually right on the ridge that runs along the side of the tube. I never find something that would have punctured the tube in the tire, or sign of penetration of the tire. They're past the part of the tire a liner would protect. Sometimes this happens repeatedly, every day or 2 or 3, on a different place, on the same tube, often when the tube on the other wheel has no problem (i.e., I don't encounter lots of thorns.)

I assume the ridges that run along the tube are artifacts of manufacture, not seams, but I don't know how they're made; maybe they can be flimsier. I've also wondered if they aren't, perhaps, at the edge of the liner and a defect in the liner does the dirty work. I inspect the liner for flaws in its edge; if I find one I discard it. Perhaps they merely rub the tube the wrong way occasionally.