I was deep underground in the flat world tunneler's dream preset and there appeared to be a cloud-like formation floating in the hole I made. From the bottom, it looks like the sky, and from the top of it, it looks like a cloud. This was on singleplayer.
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I can see strange block sizes in your screenshot (http://img6.imagebanana.com/img/i6gsutpf/tmp.png). Do you have mods installed?

I do not see what you mean.
Also those sizes look odd because of his field of view and the angle its taken.

I see nothing out of the ordinary in that screenshot.

Clouds man, get over it

Tunnelers dream has 230 layers of stone, the clouds are moving on layer 128 --> The clouds are moving through your tunnels

Clouds (and the sky) are magical and move through solid stone.

@Meta: No, that is the sky cutting through the stone

I made an issue about that bug already 😛
MC-997

even though it is already marked as resolved, I found out today what it is caused by.
you can see the sky because you see the clouds there. When looking through clouds from underneath, they hide all blocks above and show the sky.