The scratch isn't a defect, it's just a typical scratch from handling lambskin leather - it can just be buffed out. However the flap on the square mini is misaligned. It isn't a defect per se but back in December, I saw the exact same black square mini in Berlin and the flap was misaligned. The left part noticeably sitting lower. The SA showed me another one as they received 2 that morning, and it had the same problem. The black square minis are hard to come by but I passed on both. 2 weeks later, I was in Milan, happen to see another black square mini - same thing. I think there was just a bad batch of black square minis with the uneven flaps.
If it bothers you, I would try to bring it to your local Chanel and see if you can exchange it. Provided you have all the receipts.