I guess I don't know how to relay what my issue is so please let me ask this...are there any rules that should be followed so as not to prevent your breeders from doing the deed? I didn't know I would ever have this issue and haven't really ever heard of it. I think its some sort of stress but I don't really see how it could affect them only when their confined. Maybe not relevant but out of those 50 or so hens, I'm averaging around a dozen eggs per day

I rarely get 2 dozen and somedays only get 10...very discouraging
Please try to forget whether I'm right or wrong about the birds breeding while locked up...they aren't. Muddy feet would leave all the evidence needed.
I think what's confusing all of us is that we, too have white chickens. And we have fertilized eggs from those white chickens. And we have muddy times, at our houses, too. These aren't alien concepts to us.
Contrary to what you've said, I have personally seen a rooster mount a white hen in the mud and the hen's back was not muddy. Heck, our pasture is always muddy all spring, and sometimes I have problems with muddy footprints staining my eggs, but I don't have any muddy backed hens. Unless your birds are literally sitting in muddy soup and their undersides are caked with mud (and if this is the case, you have bigger problems than your breeding pens), I don't see why you would expect muddy footprints on your hens.
From your description, there is nothing about your pens that will stop a rooster from mating hens. Many people keep show chickens in little cages not much bigger than a rabbit hutch, just a few square feet per chicken, and add the rooster when it's time to have fertile eggs. The small space doesn't stop the rooster from doing his business.
If you truly want to know if they are mating in the small pens, you'll have to run the experiment of leaving a group locked in the small pen for at least two, but possibly three, weeks and then crack the eggs and check for fertility. And/or you could set up a camera. If you don't want to do these things, then I'm not sure anyone can help you, and since you already know you have fertile eggs, maybe it doesn't really matter.
As far as your egg numbers, have you seen this thread?
https://www.backyardchickens.com/t/423023/why-arent-my-chickens-laying-here-are-your-answers