What you are seeing is not that unusual, no matter how clean you keep the nests or how well behaved your chickens are. Those eggs are OK to use.
The hen puts a wet coating on the egg when it is laid, called bloom. It quickly dries and makes it harder for bacteria to get inside. It doesn’t make it impossible for bacteria to get inside but it is pretty effective. If you wash the egg or scratch it you can remove the bloom. That doesn’t mean bacteria immediately rush inside, just that it is easier for them to get inside.
Once bacteria get inside, they need two conditions to start multiplying, food and temperature. The egg itself is a perfect food for them. Egg is often what scientists use to culture bacteria. You can’t do anything about that egg providing them the perfect food source. But you can affect the temperature. The cooler the egg is the slower the bacteria grows. Keeping the egg in your refrigerator really slows down that bacteria growth.
The way I handle it, I keep any clean eggs on my kitchen counter, usually for no more than two weeks. Any dirty eggs get washed and stored in the refrigerator, again usually for not much more than two weeks, though they can probably go for a couple of months either place without a problem.
When you wash an egg, the recommendation is to use water a little warmer than the egg. I just run the tap until the water has warmed. Ten degrees warmer is plenty. The reason to use warm water is that the egg has an air cell. If the air in that air cell gets cooler, it shrinks and the suction can maybe draw in bacteria from outside the egg, like the dirty wash water. If you use warmer water the air expands, creating a pressure on the egg and keeping that dirty wash water out. When the egg cools off later and creates suction, supposedly the outside of the egg is clean so no bacteria get pulled inside.
Hope this helps a bit. Glad you asked. I haven't seen this topic covered lately and it is well worth discussing.