Could be a coon, dog, or fox. They'll all dig to get at prey. Coon or fox could also climb that fence quite easily, and make off with the duck without digging a hole to get in. Climbing it would be easier than digging.
When using soft wire, we always have a bottom bar or board.
That discourages most diggers.
We have wild pigs, so we put our yard fence on a concrete border and even then, the pigs one night almost tore a hole in the heavy chain link and may have if I had not heard them and turned the lights on and went to look, scaring them.
No telling what got into your pen, maybe look for tracks?