I think an egg would go rotten because 1) it wasn't fertile in the first place, or 2) it had a problem developing, or 3) it wasn't sat on consistently and the duckling died. If an egg like that got sat on the warmth would help bacteria to grow. A healthy living egg would fight off the bacteria to some degree. I don't think there is anything you can do to keep more eggs from going rotten at this point - IF they were going to go rotten.
I don't know the answer to your question about rotten eggs breaking over the other eggs. I know that's not good in an incubator, but it may not be as big a problem when you have broody hens hatching the eggs instead because it's not an inclosed environment like in an incubator. I hope someone else can help you with this question though.