Plywood will seldem be thinner than it was new, it does come in many thicknesses sanded and unsanded.I would try again for plywood that matches, you don't need a ridge there.
You are right, it was my bad: I probably mismatched some of them. So, I did what I should have done since day and measured them with my digital caliper. The present ones measure around .48 inches, and some of the new ones I was using measured .59 inches. I am in the process of replacing the .59 inch ones.