Many cats don't like the food and water close together because they don't want to smell the food while they're drinking. When they smell the food (and they aren't eating), it triggers the need to cover in order to avoid predators (real or imagined) being attracted to the nest. In general, double dishes are not a good idea for cats. Another problem with double dishes is that food particles can get dropped in the water, which causes contamination. You may also have a dish that's too deep. Your cat may have to stick his head too far into the dish to get to the food. After separating the food and water, if your cat still exhibits the behavior, switch to a shallow dish.