My first thought with your multiple issues would be inconsistency in the incubator, mainly temperatures up and down, and/or humidity up and down. But having many hatch without issues, would more likely point back to the parents of the eggs. Anything from genetics to feed, etc could be an issue. In other words, it’s really hard to guess! Lol
I will say the duckling pictured doesn’t look too awfully bad, though I’m on my phone and the pics don’t look very clear to me. The one I had, you saw my thread, he is now 2 years old with a much, much worse deformity. (I did recently give him away, along with several other extra drakes, I had wayyyy too many boys!) Over the years, I’ve had 2 or 3 hatch with deformed bills and only the one survived and thrived. But looking around this site, you’ll find many deformities that can be overcome.
Ducklings bills are somewhat soft when they first hatch, so it’s possible that it will improve, or even get worse. So I would suggest that you monitor it and make sure the duckling can eat and drink without any problems and pray for the best! Looks like a beautiful little fella.