I have watched the farmer put fish in the bin and the count goes up but when she puts fruit in there is no change.
As soon as your farmer picks the fruit, the food count goes up. Your farmer does not need to carry the fruit to the bin for it to be counted. S/he just has to pick it off the tree. Look carefully when the farmer picks the fruit and you'll see your food count go up immediately. The drop is from your villagers eating.