I have found that first time mums to be scared of their offspring, attacking them in fright, trying to protect herself. She may have nipped the skin with her teeth in trying to clean them. The eye infection could be due to being poked in the eye by a sharp piece of hay, for this reason we allways used old towels, and as they got older slowly introducing, hay and woodshavings.
Rats and mice would have killed the babies had it been them, the chances are a good mother would fight them off, i saw one of my bucks this morning chasing a dog rat away from the hens so i know they can do it.
You could clean the wounds with a weak, salt soultion then rub with a child strength antispetic and try to stop the mother from licking the area