From a behavioral standpoint, cats usually cover their waste when in strange territory or to acknowledge the higher position of another cat that uses that range. Other cats may leave waste uncovered as a signal that they "own" the territory, and proclaim their dominance. In most cases, cats that live with humans and use litter boxes tend to cover up their waste, When more than one cat is in the household, sometimes one will start signaling ownership by leaving waste uncovered.
In this case, it may be related to the type of litter. This litter may be uncomfortable for their paws to dig. Paw pads are one of the most sensitive parts of the cat's body--they use paw pats to test temperature, texture, and movement of objects. There is a wide variety of cat box fillers, from gravel-type clay products or recycled paper pellets, to fine-grained clumping types made from clay to corn or wheat. If the litter you provide is one of the heavier, rougher textures, it may help to try a less abrasive type. If you do decide to switch litters, do so very gradually. Combine the new with the old type of litter, in a 50/50 mix, and each week add a greater percentage of the new and less of the old type. Just a couple of thoughts.