I have come to the same problem of taking down both predators and prey and I'm unable to harvest from them with my skinning knife. It's not due to the level of my knife because it would work on one hippo and not the other. Also have the same issue when I take down crowned animals. when it comes to harvesting it doesn't drop any loot or remove carcass.
Not just the marshes; when killing 4 or more creatures often one will not be able to be harvested, will just lay there and not be interactable. Occasionally this happens with bosses, very frustrating