It's hard to deal with these things for your first clutch. Sorry to hear that some of them didn't make it.
It's pretty much a "rule" to let the babies come out of the egg by themselves.
I've seen babies pip and stay in the egg for another 5 days or so. Some others come out the same day they pip.
Also, alot of babies will coil in the eggs very firmly and not move at all. I've often wondered if my straglers are dead in the egg, then they emerge several days after their siblings.
Every one breeding will have slugs, still borns, deformed babies, etc..
Sorry again to hear you are having to deal with this.