That is odd. With only 12 villagers even one farmer should be able to keep up without any problem. What speed setting are you using? Is your farmer or farmers perhaps ignoring the crops and harvesting just the coconuts? Not only does it take longer for the farmer to deliver each nut, it's worth less food points than the crops.

A further thought: did this happen while your game was off? Your farmer/s may have fallen ill and were healed by a doctor only after some time had gone by, so they were unable to work. If you've not turned off the game in the interval, your log text might confirm this, or give some other clues. See the sticky thread about the log files here.