This stone with at least one artificially cup mark lays in the Center Court of the Minoan Palace of Malia (Crete). It's situated not far away from a room with a so called stone offering table (Kernos), but that doesn't mean it is in any way related to this table.
Cup marks can have very different reasons. Some holes in stones evolve from day by day use – like a counter bearing of a door. Some shallow holes are placed in a specific spot in a specific way for a specific purpose – whatever purpose it may have been. Some cups marks are a religious form of vandalism, because most pilgrims want to bring home some original dust as a reminder and relic from a holy place. They will harvest the "holy dust" by scratching with a sharp object from an already by other fanatics shallow spots marked place. More and more visitors will do that and in the end they will produce "pockmarked" stones around and inside holy places.
Whatever purpose this "canon ball" with a cup mark once had – I don't know. At least I posted a picture of something with "cup" in it, without being a obvious and real cup.