Just because the egg is clear does not mean it was not fertile. In general, if your eggs don’t develop or stop development in the first week, it’s probably due to something that happened before incubation started. If they quit the last week, it’s normally something to do with your incubation.
Check for fertility. If the eggs you open are fertile, the eggs you don’t open are probably fertile too. Here’s a good link with photos of what to look for.
Fertile Egg Photos
https://www.backyardchickens.com/t/16008/how-to-tell-a-fertile-vs-infertile-egg-pictures
If the eggs are fertile, that means the embryo was alive when the egg was laid. Disease or nutrition can cause some problems, but let’s look at how you handle them before you start them in the incubator.
How long do you store them? At what temperatures? Too hot, too cold, or too long can cause problems. Do you have a cycle where temperatures going from warm to cool and back to warm. Cycling temperatures like that can damage the embryo. I’d keep them out of sun and out of vents blowing on them and try to keep them about the same temperatures. Try not to shake them either.
Not turning them is not something that will keep them from developing. Those problems show up later when the chick develops but doesn’t hatch. If they are not developing how you turn them is not your problem.
If the eggs are not fertile, that can mean a fertility problem with your rooster. Disease or injury can cause a problem, anything from frostbite to an injury from a predator attack.
Age can cause infertility, in both hens and roosters. If yours are four years old or more, this is something to consider. Not all old hens and roosters are infertile, just some.
How old are they? A mature hen may not allow an immature rooster to mate. So if your hens are older and your rooster is just a teenager, this might be the problem.
What breeds do you have or the real question is how thick are their feathers? On chickens with really thick feathers, usually show-quality Orpington or cochin, something like that, the feathers can be so thick the rooster has trouble hitting the target. Some serious breeders of top quality show birds have been known to trim the feathers around the vent or just pluck them out to give the rooster a better target. Most hatchery quality chickens even of the thick-feathered breeds won’t have this problem, but you never know.
Chickens laying eggs intended to be hatched need to get certain vitamins and minerals in trace amounts. You should get better hatch rates than you are getting on just pure Layer feed. I’m not sure nutrition is your problem. Still, it won’t hurt to work on it.
The eggs are a good nutritious treat for them, but if they are not eating those trace vitamins and minerals to start with, their eggs won’t contain them. There is nothing wrong with feeding them the eggs, but a little green stuff, grass, lettuce, cabbage, chard, Kale, spinach, or stuff like that is a good idea. Or feed them your kitchen scraps. They can eat practically anything you eat and it will have nutrients that Layer doesn’t have. If they are foraging for some of their own food, they should be getting all these vitamins and minerals they need.
Obviously I don’t know why your eggs are not developing. There are a whole lot of possible causes. I sure wish you luck sorting it out.
