I feel like I was facing the same issue. 10 of my 31 (I originally set 42/6 not fertile/5 quit early) eggs didn’t hatch and I feel like it had to do with all of the hatched ducklings trampling over the eggs. The 10 were alive and well the day that hatching began.
I eventually opened the incubator and removed egg shells and ducklings but that could have caused some shrink wrapping. I had to assist one due to that. I should have inspected the dead unhatched ducklings. I still ended up with 21 but it would have been nicer if I would have had more hatch.
Definitely utilizing a brooder earlier next time! Just need to figure out how to salvage the humidity levels. I even turned on the shower and steamed up the bathroom