What would cause this weird bearing wear?

You NEVER pry on the rod cap. When I cycle rods (in a fixture - not in an engine) I use the handle of my soft dead blow to loosen the cap. It's hard to dssecribe but it doesn't take any real effort and the force is applied (tapping lightly) on the sides of the saddle. It can be done with the bearing in place - you don't hit the bearing - just the cap. In any event - if there are marks there that can catch a finger nail they need to be take out. Any mismatch in the surface can cause the cap to go on cocked affecting clearance and lessens the ability of the rod to do it's job.