This may be an issue with /clone and /fill or it could just be a general issue...
As seen in these images: http://imgur.com/a/0PoT1 the sky light level is not always changed by blocks above the player.
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Comments
Erik Broes
Piraka~Mistika
...It seems to have either updated itself or been fixed in 14w04a.
I still have this issue in 14w05b.
I still have this issue in 14w21b, can a mod please reopen it?
Temporary fix: open the world in mcedit, select the affected chunks. Click the relight button, save.
build the 'filled' area by hand; see if it still happens.