Are you seeing a lot of feathers on the ground? I didn't think my Muscovy's were starting molt yet till 3 got in the pool the other day and left quite a few feathers behind when they got out.
But again if they are in a run with out hardware cloth around it at night good chance something could stick their arm through and grab a duck usually a coon but you'd find a headless duck in the morning a mink or weasel can get through very small opening and they do not leave live ducks behind when they leave. It is said a mink can get through a 1" opening.