With as many birds as I've had, I've experienced probably every poultry reproductive issue out there. From my experience, shell quality issues fall into three types, dietary, transmissible, organic.
Dietary generally affect more than one bird in the flock and are typically caused by low dietary calcium, excessive dietary calcium, or general poor diet. Underdog hens who don't get enough food from the feeders also fall into this category. Even though I have a lot of feeder space, I also have some real butthead alpha hens.
Transmissible, such as IB, affect some of the birds and often comes on suddenly. Some birds may be affected for life and should be culled, others make a recovery and resume normal shell quality and rate of lay.
Organic includes poor shell quality during early and late molt, tumors, reproductive injury, nest crowding, old age, parasite loads, and other non-disease, non-dietary issues. While you can correct some of these, others require time and some cannot be resolved. A bird that begins to lay eggs with a single defect, such as a spiral at the large end or a groove along the length, may carry that flaw forever, and it makes for a unique egg basket.
I have one hen that lays an egg that has a flat spot on the bottom and wrinkles along the sides, as if it was dropped soft and tried to "splash" then hardened. She doesn't lay many, but they are all like that.
