I would have culled too, once I saw the opened sore. Looks systemic. I would take them to be infected cysts of some kind and, if there are lots of them, not good for fur or meat that way, so cull.
I can think of a few things that would be, all of them cause recurring cysts like that and, all can become cancers, two are carried by rats, the others genetic so, I'd lean toward the rats in this case since others in the litter are not showing any cysts. Perhaps that one just had a slightly weaker immune system and, got it form the rats while the others have a stronger immune system and are fine.