They may have just not been strong embryos. A temp change maybe. They just weren't meant to be. You can leave the bad eggs if you don't want to cut them away. A good egg won't grow mold. We have a couple burm eggs going bad now that are stuck to good eggs. The good eggs candle great and have no mold at all while the bad ones are covered. But we cant get them apart. Sooo we left them.
If you can get the good egg away from the others you can. Just be careful and don't take to long with them out of the bator.
Good luck.