Yes, poop balls do cause issues. I hope you can get a handle on it. :-)
Also, vitamin deficiencies can cause pads to be thin and infect easily. So make sure to keep them on a good quail diet. I think you are keeping them in a good way, but keep the ones with the pad issues on something soft...
Bumblefoot is just a term for infections in the feet. And they do not necessarily have to have that common black dot on the pad. That looks like the pads have become very irritated and infected as well. I think the wire is bruising their feet. What size of wire floor are you using...1/4 inch...