Hmmm tasty....
Getting the occasional fertilised egg is a risk you take if you get proper free range. it's no big deal (unless it's your last egg), you can also occasionally get eggs that have a soft membrane instead of a hard shell round them, they'll never make it to the shops but if you have your own chickens you'll see them (the membrane eggs are perfectly OK to eat.)
You just have to accept that nature doesn't always make things exactly as we'd like them to be.