I also hold a personal belief that disturbing the eggs/babies can lead to issues like this. This isn't to say that I blame the breeder when they have issues with their babies. Not at all.
However, it's part of the reason I will be letting my females naturally incubate their own clutches when they finally have them. And I won't be cutting the eggs, nor will I be candling them.
I believe that keeping the process as natural as possible, and disturbing the nest as little as possible, will yield better results.