How strange to get the same question from two different people with the same email address just a few minutes apart. Get a countersink, remove the screws, countersink the holes, and rescrew. You can buy a countersink at any tool supplier. You might get a good screwdriver that fits good and use a little force on the screws. You also might get a 3/8" drill bit and drill just into the top for a countersink. You may be able to stick a big phillips screwdriver and twist it around a few times to make your countersink.
While the thinset would technically cover it, the tile will sit on the screw and later on when you set a pan, etc. down wrong on the wrong place on the tile, it may crack on you.