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It doesn't matter if a rabbit is being raised as a pet or for the meat. A bored rabbit will act out in many ways. Throwing around food or litter, charging a person who comes into their personal space, chewing on wire, biting, fighting ... They need something to do or they do unacceptable things. A male will hit the stage where he believes himself to be king of all he sees. When this happens he'll fight other males, who have the same attitude he does, and they will bloody each other. If I were to guess I'd say your rabbit was disciplining your ducks for failing to display proper behavior towards him. Not that they ever could but it doesn't stop the rabbit from expecting it. They have rules and communication that evolve from being prey animals. Most rabbits will come around if a person finds a way to rub their nose or scratch around their ears. That is because it's the kind of behavior expected from a submissive rabbit.
My ducklings are currently sharing my rabbits room. She's acting out and depressed and uncertain of her place. The ducklings are enclosed and Dixie still has her litter box and toys with freedom to move around yet has started spending most of her time in a box instead of sprawled out in the middle of her rug as queen of all she sees. She'll watch me with the ducklings and come to the fence for attention then turn her back on me and thump, signaling her displeasure. She's started using a spot closest to the duck enclosure to drop copious amounts of droppings as a territory mark. And when I spend time sitting with her as I do daily, she'll sniff and bump all the way around me then go into a box and thump. LOL I have an awful lot of making up to do with her once the ducklings are outside for good.