Runny eggs in commercial flocks is from high levels of ammonia in the air (when ventilation is not well managed), and the age of the eggs when we get them.
MG etc. is common in commercial laying flocks, and backyard flocks. The last time my birds were tested for it, I was surprised to learn they tested negative. I expected a positive because of how common it is. The more concerning diseases are going to be evident.
Any disease agent that can damage the reproductive tract or severely inhibit the health of the bird can cause egg quality concerns. Infectious Bronchitis is famous for causing egg quality concerns, but I cannot imagine having this problem and not knowing.
If it is a persistent problem over multiple birds, any ventilation (ammonia) concerns settled, the eggs were collected promptly, Not allowed to withstand temperatures well below freezing, the eggs were eaten fresh, they were visibly healthy, and their was still a persistent problem, then I would suspect a disease agent that has colonized the reproductive tract. I would cull a "guilty" individual and examine the reproductive tract for signs of disease. Bedding in poor condition could be a source of such an infection.
Can cocci cause egg quality problems? E. Coli?
Most of the time runny eggs are a problem in a backyard flock it is either due to old hens, older eggs, high heat, or bedding in poor condition without adequate ventilation.
Similar to what others mentioned, I would assume it was management until I seen evidence otherwise.