So I think I made a breakthrough discovery on this issue related to my reloads at least. What I found was that the few that are failing case gauge right at the rim have very small almost imperceptible deformations on the outside edge of the case rim from prior extraction. The deformation is small enough that on some I can force them into the gauge and it flattens the flawed area enough to go in. To verify this I took one with the issue and lightly sanded the edge of the rim where the issue was and it fit fine in the gauge.
Something to check on those that aren't sizing or crimp related.