Are there any tiny cracks where the rough spot is? Can you candle the egg and see if the duckling is in the air cell at the top (fat end) of the egg? Another way to check if it is indeed internally pipped and preparing to hatch is to very very gently scratch on the egg with your fingernail and hold it up to your ear. If you hear tapping or peeping coming from inside the egg, it is internally pipped and should start to hatch out in the next day or so.
Is there any way the eggs could have been incubated before you put them into your incubator? Like by a hen? Otherwise, hatching at 21 days is pretty unlikely, so it might just be moving around in there.