I'm wondering if this might be something like trench foot in humans. Ducklings are very wet, and if they weren't taking good care of them and weren't changing out the brooder, the duckling may have been living in a perpetually wet brooder that also had a lot of poop mixed in, adding ammonia to the mix - not a good situation.

I would make sure to keep the brooder very, very dry - build a special duckling waterer to keep the splashing down and if you see the brooder getting even a little damp, change it.

Additionally, applying heat to the foot for up to five minutes might help with circulation and is suggested when humans have trench foot. That could be done by allowing the duckling to swim in warm water for five minutes, then taking it out and thoroughly drying the foot off.

Applying an antibacterial cream is a good idea too, which I see you've already done.
 

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