My bag has scratches, is it damaged?

Leather is a natural product and will vary from hide to hide and even within a hide. Bags that have a seam in the center most likely will not be an exact match. This is not a flaw in the bag, it is just how leather works. We do our best to make the leathers match as close as possible but because of variance in each hide it is not always possible.
This is a snippet from one of our suppliers FAQ's about distressed leather:

My bag has scratches, is it damaged?

No, this is a beautiful feature of natural leather and the markings will be unique to you. All products are lightly treated so the natural characteristics of the hide can be showcased. Since the sealant is breathable, the leather will patina over time and any scratches that occur will work themselves out. If you want to accelerate a scratch removal, you can either set the bag indirectly from a heat source to warm the wax in the finish. With a damp cloth, rub the scratch out.

Here are examples of natural marks and variations on hides.