Naturally, rabbits and small rodents usually have a special apartment in their burrow, warrens or whatever that is used as a latrine. It has no idea that that thing in its hutch is going to be used to put the food in next time and seeing there is no sand/earth to use, it is using the bowl trying to 'separate' the latrine from its living quarters. There in no intelligence involved, merely instinct.
It is something that has always annoyed me about those people who build hutches/cages etc. professionally. They could at least find out about the animals they are constructing items for. The cage builders for birds are the same, the most ornate and expensive cages are almost always totally unsuitable for birds.