Not sure if this is me being stupid or if this is a bug, but it looks like whenever food rots in my storage building (stone roofed building above the farm), the rotted food spawns on the roof instead of on the floor of the building/in any of the storage containers I have in there. I think this might be because I've completely filled the room with clay pots? I'm not 100% sure but regardless I noticed and figured I would share.
This should be fixed for the next update. Thanks for reporting! :)