Not sure exactly what your procedure is for helping chicks out of the shell, but something that often happens during that process is that the peachick gets "shrink-wrapped" -- there is some moisture loss inside the membrane, or the outside of the membrane starts to dry out and cling to the chick.  That makes it harder (or impossible) for the chick to turn inside the egg which it needs to do in order to hatch normally.  The chick ends up stuck and spends longer inside the shell.  Sometimes it's unavoidable, sometimes it just happens, and sometimes an improvement in or adjustment to the technique can head it off.  When the chick is in the shell longer, the feet start to harden and then you have the curled foot (curled toes) issue to fix after the chick hatches.
 
Everything we do in artificial incubation is an imitation of how it works with the peahen -- but peahens are optimized for making chicks, and frankly better at it.  We are a distant second with our mechanical methods -- I doubt if any incubator made can maintain body temperature as accurately as a peahen.
 
A certain number of artificially hatched chicks will fail regardless.  Some will only hatch with intervention.  Knowing when to intervene is difficult, and even well-meaning and/or necessary interventions come with their own risks and costs.  Even the peahen will have some eggs which fail.  Peafowl are more difficult to hatch than chickens!