Occasionally when you build you build on a tile the improvement has no effect. This is noticeable when you build farms on farming bonus tiles.
Example :- You build a farm on a farming bonus tile but the food producton is unchanged. The tile can be used for other improvements and still work, but effectively it is a 'dead' tile for farming.
Not sure if anything can be done, it effects prolly less than 5% of the farming tiles.