That makes actually sense, thanks redstonehelper.
I cannot reproduce this bug in 1.9. If you once lightened that area up, will it then become dark again, after reloading the chunks?
MC-29490 does not even reproduce in my version of Minecraft. (Just tested seed -6675450379693409235 as in the description)
How is this a duplicate of black random spots on the map? You never find such huge black and straight areas as on my pictures.
Something has changed. From Minecraft 1.10 on, the problem shown in the pictures __1.png and __2.png from 27/Mar/2016 (on my server) is gone. The lighting there is now as it should be. This includes the current version Minecraft 1.11.2.