I guess your are on despotism. Despotism incurs tile output penalty, any tile producing more than 2 of anything
(food, prod, gold) will suffer -1 penalty. Normaly grassland produce 2 food, you irigate it's up to 3, but due to penalty city
can still only use 2. You need to changes government (and reaserch it first). This is all in wiki I believe.