16 eggs from 1 hen means you collected for nearly 3 weeks. That's too long for good results. Some from the fridge means that some were kept too cold. Some not in the fridge may have been kept too warm. 50 to 60 for up to 2 weeks ( 1 week preferable) if all other conditions during the incubation were perfect your results may have been better.
Sounds like the egg prep was the issue.
Also, I believe that when storing they should be turned daily.
Rooster fertility, roo, hen ratio, breeder age, daylength, parasites, nutrition and MANY other things play a role.
1+1 does not always equal 2.