A lot of my cats have done this when they're done eating. It's either that they've had enough and are 'burying' the rest for later or that they don't think much of the flavour/fancy something different (very picky 13yo boy ) and are 'burying' it to get rid of the nasty smell
Mooch has done this since she was a kitten. I learned quick not to put the food too close to the water bowl! She'd make a huge mess just scooping water right out of it while "burying" her leftovers. She prefers to graze; and as others have said, this is what they do to hide their leftovers. Noodles prefers to eat everything in one sitting and has never tried to cover her leftovers.
Sophie does this too. Their food bowls are on the kitchen table and she will scratch at the table top sometimes. The fountain that they drink from is on the kitchen floor so they are nowhere near each other. I wonder if she wants me to move her dish further away from Lilith's although she usually eats first and will eat some out of each dish before leaving the table. At first I thought she didn't like the feel of the tablecloth under her feet so I removed it but she still does it. Lilith does not do this. Sometimes they eat at the same time and have never had any issues with it. She only seems to do that when Lilith is not eating at the same time as her.