I cannot tell you why this happened. Sorry. But I have a few questions and pointers that might help you in the future.
If I have eggs that have not hatched, there are a few things I do before I decide they are toast.
1) in a quiet place, hold the egg to your ear. If you hear scratching or tapping noises, put the egg back. Tap the egg with your finger, sometimes this will make the chick squeak. If you hear anything, put the egg back in the bator.
2) candle the egg. Shine your light into the fat end. There will be a dark, solid mass below and your light will fill the air space in the fat end. Tap the egg. Watch to see if there is any movement in the fat end, a bumping around. If you see movement, even with no noise, put the egg back.
3) if you candle the egg and the fat end is hazy looking, there is a good chance that chick pipped and drowned. Liquid in the fat end looks hazy and the line between dark and light, the line between above and below the airsac looks mirky and not sharply defined, this usually means too much liquid and a dead egg. This is also a very good clue all throughout the hatch when you candle. The line between air sac and egg contents (yolk, white, chick) should be sharp, well defined and very distinct. When that line gets hazy and smudgey, that egg is dead.
4) when I open a suspect egg that should have hatched, I do it in a very specific way. I make a tiny hole in the FAT END. I enlarge the hole carefully to get my finger in. You should see a white membrane (dry looking) with the lump of a chick below. Reach in and give the chick a poke. If it wiggles, or feels soft and giving, put the egg back in the bator. If it feels hard and there is no wiggling, the chick is dead. I have had chicks hatch from eggs I have opened at the fat end. They are at higher risk for drying onto their shells, so you will have to be vigilant and make sure they don't stick...but sticking is a risk with slow chicks anyway. But if you just crack the shell like you are going to fry the egg, then the chick has no chance.
My number one reason for chicks that hatch late is too low temps. My number one reason for chicks who make it 21 days and die at the finish line is too much humidity and they drown in their shells. You should never toss ANY egg without looking in it. If you crack and find lots of dead chicks that are surrounded by thick slime, there is too much humidity in your bator. Chicks should be moist, not slimey.
You said you cracked eggs and found live chicks. Were they moving? I have found that with the yolk sacs, it's the work of hatching that seems to draw the yolk sack into their bodies over the last several hours. I have removed chicks from eggs but if that yolk sac is mostly out, they rarely survive. The longer a chick boots his way out of his own egg, the better off he is. So I will half hatch some, and leave their bottom half in the egg to kick their own way out. Also, if you attempt to rescue a chick and there is bleeding from the membrane, STOP and apply a little (gentle) direct pressure to the bleeder. A chick will bleed to death through its membrane. A membrane that is still rich with blood tells you the chick is NOT ready to hatch! WHen it is ready, that blood has been drawn into the body. A blood filled membrane is a premature chick.
Sorry about this. Hatching is hit and miss for some of us. I hope it goes better next time.