How to reproduce:

Go to biomes with trees or just plant some trees.

Place(fill) some blocks at Y=96 or above.

Then, the ground under the trees gets dark (only in chunk where the block was placed).  Apparently, sunlight does not spread horizontally (it only spreads vertically).

The bottom of the filled block is completely dark(light level=0).

Sometimes this happen under Y=96, but it is more difficult to reproduce.