Could also be pin feathers growing in, they can be 'uncomfortable',
one must be very careful handling a bird full of pin feathers.
Plus most chicks and chickens really don't like to be handled much,
it's the natural 'flight' reaction of a prey animal.
Even with frequent and consistent handling some will never come to enjoy it.
And they can change their minds too, have had chicks that loved to be picked up all if sudden not like it....and also chicks that hated being handled come up and apparently want to be touched and picked up. Just recently had a pullet start to hang out on the roost or perch next to me letting me touch her all over where before she was one of the most skittish birds in the flock. SMH<shrugs> ya just never know with live animals.