They look like infected cuts, and they look several days old- if you are positive that the brooder has no sharp wire ect that the ducklings can get to, my guess is the problem is in the incubator. I assume they were in there for a few hours after they hatched to dry off? The foot in the photo looks bad, this bird needs care (cleaning, padding, kept dry, antibiotics- preferably systemic, if not, at least cleaned and topical) so hopefully it won't be crippled as an adult. Ducks are heavy bodied birds- they do best with two functional feet. Infected feet can also happen if the ducklings are kept on soiled bedding for prolonged periods of time, the photo of the brooder is very nice- but how often are you cleaning/changing the liner?