I returned a Boy bag last year because of a similar issue. It too, had what looked like a rip at a stitch. It was difficult to see but I could feel it and it annoyed me greatly that I had just spent $6000 on a bag that wasn't perfect. It was more apparent in a zoomed in picture.
I returned it without difficulty but unfortunately I missed out on a replacement red caviar boy as they has sold out. I got a beautiful blue lambskin boy instead. I adore him but I still desperately want a red cross body chanel bag. So be quick if you want like for like.
Good luck.