What would cause a ryukin goldfish to have a missing eye and red gills?

Yesterday I had two goldfish shipped to my house. One of the goldfish was perfectly fine and has adjusted to the new tank. The other calico ryukin came missing an eye. I didn't notice any gill problems until I watched him swim around in the tank. He doesn't appear to be in any immediate distress other than missing an eye and being half blind, the gill redness has not progressed. He is not gasping for air and eats and swims with the others just slower and well like a half blind fish would. The company has refunded my money for the fish but my concern right now is the gills. I know redness usual indicates ammonia poisoning. There was a lot of poop in the bag is it possible when I opened the bag after floating them that when the poop hit the air it created ammonia in the bag? Also I plan to move the small healthy ryukin to my 25 gallon tank and keep the injured one in the 12 gallon with some aquarium salt. Will the redness ever go away if the fish heals? Could it possibly be caused from some kind of trauma to the head from being shipped? Or maybe air pressure from the cabin? (Although I was told the styrofoam container was somehow pressurized). Is it some kind of disease maybe? Anyways I feel bad for having fish shipped now. Any ADVICE (not opinions, or criticism) would help.