If you have a volume you want to clone over that has a light source already in it, say torches, and the new clone area does not have a light source, then when you clone the not lit volume on to the lit volume, the blocks will still be lit up without the actual light source there. If you place a block where the light source was before the clone, the light from the block goes away, like it should.
I made it a video here: http://youtu.be/LzToDvBbQ9U
Related issues
is duplicated by
Comments


The /clone command,
/clone -473 63 165 -467 67 207 20 60 -22.
It's activated by a /testfor block first,
/testfor @p[19,58,-25,dx=8,dy=13,dz=45]

I can confirm this issue. It also happens the other way around, sometimes blocks stay dark after cloning.

Confirmed for 1.8. Also affects /fill. At least for /fill, the light is client-side/fixes itself after relogging.

Maybe this should be merged with MC-46129 (or the other way around).

An explanation of why this happens & a fix can be found here: https://github.com/MinecraftForge/MinecraftForge/pull/3870
See below

This bug has already been fixed: To reproduce this precise issue, use version 14w21b and do the following:
Place a torch
Clone a large area (~4000 blocks) of air onto the torch
The light is still there, even after relogging
However, many of the linked issues are NOT duplicates of this one, see MC-117094 for more details
Which command did you perform? 🙂