On a server with an amplified world.
A 9x9 farm with 1 water source in the center. Under the water is a glass block with a lava source under that. Around the farm are a total of 8 torches. I've done farms like this many many times before and never had this problem.

The problem is that there are 4 places that the crops will not grow, which you can see in the screen shot included.
Starting from left to right are: 2 potatoes, 2 beetroot, 4 wheat.
The rows were filled with others of the same crop and they grew with no problem.