We've had this problem too. Sometimes we catch our Border Collie chowing down on something he found in the field. Most often it's disgusting, like a dead animal, or cat or rabbit turds, but twice he was eating a nest of baby bunnies. I guess they're a delicacy, even though he leaves the adult rabbits alone and shows no interest in catching them. The first time we dragged him away in time to save most of them, the second time he ate them all before we could stop him.
Many year ago (with a different dog, a retriever type with a gentle mouth) she ran up to me, all proud and wagging, with some animal in her mouth. It was moving around, but barely struggling, so my first thought was, "Oh no, she caught a rat but it looks injured, now I'm going to have to finish it off." But on closer inspection, it was a tiny baby bunny that didn't look like it had any injury. My dog willingly gave me the bunny (lots of praise for that) and I took it to the area she had been sniffing and digging, and to my amazement, I found the nest with four other baby bunnies in it! I put this one back with the others and hoped for the best.
The next day I went to check, and the mother bunny had moved all of them.
I think rabbits are kind of like deer, in the sense that they will secure their babies in a nest and leave periodically to find food. Then when they come back, if they sense the nest has been disturbed, they will move all of them to a new nest. Since she'd moved them all, including the one we'd put back, gave me confidence that it hadn't been badly injured.
