Steps:

Setup: Create a new world with "Caves and Cliffs" experimental gameplay activated.  I did it both in Creative and in Survival.

1) Hollow out a space that will grow a 2x2 Jungle or Spruce tree (does not matter if there is a ceiling or not, so long as it is high enough to allow for the tree to grow normally at the surface) with a Y below 0 (any y rating will do so long as it is below 0, but I did this at several layers and found it easier to spot the bug by doing it at y minus 2 as that allowed for step 4)

2) Plant the 2x2 sapling array.

3) Use bonemeal until you are content that it isn't working.

4) Remove the saplings, then add layers of dirt until y 0 is reached (make sure there is enough space above still for the tree).

5) Add saplings and use bonemeal.

Results:

These two tree types will not grow below the y 0 layer.  Dark Oaks will, and 1x1 saplings will, but not the big trees.  However, all tree types grow at y 0 and above.

Expected Results:

All trees behave the same regardless of y value.