LoweJackson (Alfa affectionado!):
The "wear" is just that; wear from abrasion of the seal across the paint.
You mentioned that this car was repainted, but you do not know the reason why. If this repaint was because of a collision, maybe the door-to-frame fit is now out of factory specification and there is misalignment between the two, causing the wear to occur. To measure this, try using an old mechanic's technique used to measure valve-head-to-piston-top clearance in an engine. Place some soft detailing clay in the door sill and close the door on it. Open the door, and with a sharp knife, cut the compressed clay at the area of the wear. If it's very thin (less than .045" or 1.1mm) you've got a problem.
More than likely, though, is the fact that the paint from the repair is "different" (different meaning by another manufacturer/vendor) than the original or that is was not cured properly and is softer than the vehicle's original paint or that does not have the proper clearcoat on it. The hardness (or lack thereof) of the paint may be the reason as well, OR a combination of the two reasons stated here.