If they were silkie eggs a Vault on the top of the head is normal. Sometimes yolk sacs prolapse - come back out. If the chick is kept safe and given time it usually dries up and falls off. Loops of bowel is different, that does happen but it's rare.
You don't mention calibrating either you hygrometer or thermometers to know their accuracy before hand. If your hygrometer was 25 degrees off(low), as my first one was - you spent the entire hatch trying to raise the humidity above 80 or 100. And excess humidity also sucks.
If you didn't calibrate your thermometer it could have been reading a degree or more HIGH, meaning your temps ran low the entire time - which causes foot deformities, slow, weak hatchlings. Low temps can cause a wide range of problems and is really common.
Check the accuracy of your equipment by calibrating them. Then give it another shot. My first hatch was fairly sad too, just one chick but I wouldn't have hatched the over 100 ( lots more but stopped counting so I don't have to admit it to Laura) healthy babies I have hatched.
It's an art, not a plug and play science, or something that you just "follow the rules" and out pop chicks.
You call fishing - fishing because it's not Catching - no guarantees.
We call it hatching because it's not Chickening - no guarantees.
I've had zero, I have had one, I have had 100% numerous times and everything in between, even on shipped eggs. I have had broodies hatch 100% and I have had numerous broodies FAIL completely, or had to rescue more than half the hatch and put them in an incubator.
Under a broody or in your home, the best that can be done is to try. Nature offers us no guarantees and sometimes we fail. You get a feel for it eventually, and sort things out. I'm sorry it was a bad start but there are people here, successfully hatching now that had three to six bad hatches before they got things sorted out. Now they do well routinely.
You can learn this, you can make it work. It won't always go well. Nature has it's own rules and flaws, no matter what you do.
Working with and caring for livestock and pets and living things of all types includes grief and failure and loss. They're worth it in the long run. But you have to persist to get to the joy.
My daughter called her Miracle after all she's been through! I hope she comes out of her problems.
