I really don't think the black dots are a new thing or a defect, I believe they are goat freckles or beauty marks and I've seen them on bags from almost every year. My fabulous '05 Turquoise First had at least one on the handle.
I do however, believe the black or brown dot beauty marks are becoming more common and it's probably due to the fact that thousands and thousands more goat skins are needed to make as many bags as they are producing now. Plus, some dark colors will just cover up these natural markings and we won't know they are there in the first place.
The leather has also always had color variations between dye batches and individual skin's absorption level as well as texture variations between the panels of leather, but it is the crafts person's responsibility for matching the pieces together in a way that looks good on the bag, not just throw a light colored handle onto and darker color bag.
These bags are made with natural materials that may have imperfections that were characteristic of the animal used. I have personally inspected hundreds of Balenciaga bags and each one is truly unique. Balenciaga bag leather is tanned to break-in quickly and look vintage with color changes from use and time that gives the bag it's own unique character.
I'm not trying to say there aren't legitimate problems with some of the bags, but if we all look close enough at all our bags we're likely going to find things that aren't perfect about them but they are just the natural features. I've learned to love the things that give a bag it's personality.