If that soothes the pain: You did everything perfect!I agree it’s weird and it makes me nervous but I reported to the hatchery right away. Here’s a pic of how I have the duck house separated. I know the older ducks can’t reach over the barrier, it’s two feet tall. I don’t think their bills can fit through to do get to the babies. I never saw babies on the wrong side of the barrier and their bodies were all on their own side when I found them. This made me reject the idea that the older birds did something to harm them. I’m considering a HWC strip across the bottom of the barrier as an extra precaution.
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You said one of the ducklings was under the heat-pad when it died - so they did not got cold and the grown-ups bills won't fit far enough through that sturdy barrier to hurt an duckling. Anyways, it is my experience that ducks rarely get excited about little ducklings, at worst they become instant-broody and want to adopt the little ones. Integrating the half grown ducks later is another story.
The only two explanations i can come up with is that they got an infection at the hatchery or during their trip. Or somebody fed them with breadcrumbs.