I know someone else has mentioned this, I just can't remember where. I was playing Deir el-Medina 3 tonight and ran across this myself. The granaries seem to get over-stuffed by about 1 or 2 units and when this happens, the food becomes invisible. It's still there, because after the bazaar lady comes to buy, the granary isn't completely full anymore and the food is visible again. I guess it doesn't technically hurt anything, it's just annoying and sometimes alarming when you think all of a sudden your granaries are empty!