You should expect some unfertilized ones, especially if you live in the northern hemisphere (i.e winter now).
Those two rotten eggs might have had a tiny crack in them, allowing bacteria to enter. Some people candle before incubating to avoid those with cracks, but as long as they don't explode in the bator (and spread the bacteria) it shouldn't be an issue for the other eggs.
Do you have an external thermometer to check the temperature-readings from the incubator? If your incubator is a few degrees cold, that can delay hatches a few days.