This is perfectly natural, if you mean what I think you mean.
I don't. I mean wrinkling on a small length scale, not creases at flex point. Take a rubber band, pull on it a bit and add a coat of wax or paint of whatever, then let go. The coating will crack or buckle. This is about what happens to my shoes.
I figured my answer was too obvious, so I hope it didn't offend. I've never heard of your problem. What I find odd is that the shoe trees cause the wrinkles to disappear. I have some lightweight Italian shoes that develop fine lines all over with wear, but shoe trees make no difference. A bit of shoe cream helps with mine -- have you tried that? Does it have any effect? Curiously, it sounds like there's an elasticity differential within the leather -- somehow the top layer is drawn less tightly than the rest. But that makes no sense. Good luck finding an answer.