While mounted on a Donkey (chested in this case) I was taking suffocation damage in a three block high space.
The floor blocks are grass, the roof blocks are Bottom Stone Slabs and Glowstone Block.

This was not an odd hit, the whole pen caused damage.
There is a virtually identical pen adjacent housing a horse.

It did not happen when on that horse in that pen. It did happen when I entered that horses pen riding the donkey.

Update: Happens on Horses often as well in 1.1.0.5 (I also updated a mistake in my Title/Description, I meant 3 block high space, NOT 2 high space, doh!)