This is likely unrelated to invisible chunks caused by slow generation as reported in MCPE-19308, which I re-reported in MCPE-30428. I'm creating this description of an unrelated bug from the comments in that ticket.

When digging a tunnel in close quarters, I'll sometimes encounter a block that looks invisible with empty space beyond (I see bright blue sky beyond even though I'm not looking up).

I don't see how slow generation would cause this. I'm moving slowly, at the rate of 1 block every second or so. In this case I don't see underground structure through the 'window' as described in MCPE-30428, but I do sometimes see silhouettes of mobs in the distance. It's almost as if the game loses track of a single block.

This occurred a couple days ago; I had just started a new survival game. After spawning for the first time, I didn't explore, I just harvested wood from a nearby tree and immediately began digging a temporary shelter using a pickaxe from the starting bonus chest. I had dug a stairway down about 4 blocks and was digging out a small room for a crafting table and a furnace, when one of the blocks on the wall became invisible, showing bright blue sky and a distant silhouette of a skeleton bobbing up and down, likely in the river near where I spawned.

I've also seen a floor block do this (not 1.2.9 but some previous 1.2.x version). The first time that happened, seeing bright sky through a hole in the floor, I thought I had broken through the bottom of the world, which shouldn't be possible in survival mode (and I hadn't dug anywhere deep enough either).

When it happens, it typically affects just 1 block. Digging out and replacing the invisible block fixes the problem.