What causes crossbeak and missing eyes?
These are possibilities.It's my understanding that high temperatures during critical periods of incubation can cause both cross beak or missing eyes but for the chick to have both when your other chicks are completely fine I think you're more likely to be contending with something genetic, bacterial, viral, something along those lines.
Poor nutrition can be another.
Were the deformed all one same breed, how many of them??
These were all shipped eggs?