You can do everything absolutely right, but they aren't always all 'meant' to make it. Things like this simply aren't that uncommon, and will happen to every breeder at some point. You will see a great deal more of this if you make a practice of cutting the eggs--if they weren't cut, those eggs would simply have failed to hatch, and would have gone bad.
Cutting them gives us a window into what went wrong, but it can be shocking to see, at times.