The cat is making it clear to you that he's frustrated with the amount of cat litter he has. More importantly, that you have to really clean it more, since it's obvious he has no more space to pee or poop cleanly.

My cats have 3 litter boxes which I clean twice a day. One of them is a bigger and they both prefer that one. If the litter gets under 15cm, I see this behaviour. They 'bury and dig' more fervently/aggressively and litter is flying everywhere while they're 'grumbling'.