Unknown protuberance (picture added)

I'd give it a tiny dab of an antiseptic ointment and check it once a day. The more you can leave it alone to sleep and get its strength up, the quicker it should recover. You do get chicks with navels like that when your incubation humidity has been too high, but as you were hatching under a broody, I don't think that's what's happened here. More likely it's because the chick came out of the egg a little too early. It can happen in chicks that hatch by themselves as well as ones that have been 'helped' out, and usually they go on to be just fine, do don't worry too much.

Last week I had an over-humidified and then shrinkwrapped duckling who had a nasty looking one of these. It healed up after the first day...
 
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It's staying under the hen and it's not really active looking... it's always putting down its head whenever i pick it up...

Why do you think it doesn't look active? Are you lifting the momma up constantly? Let the momma do her job. You don't want her to quit raising them. you should probally wait till she shows you her babies. Good Luck Michele
 

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