Long story short, when setting a large amount of blocks there seems to be issues with light updates as seen by the screenshots.

 

I've made sure I hadn't changed anything, and used the latest Spigot along with the fresh bukkit/spigot yml's. 

 

These light updates have happened in every version from 1.8 to 1.11, as I've tested all of them thoroughly. 

 

To re-create this bug, simply use WorldEdit and execute this commands.

 

//cyl bedrock 40
//hsphere bedrock 40

 

(This happens with any plugin editing a large amount of blocks)

 

Even when placing torches or other blocks, these lighting issues do not update. They are permanently there, with no fix in sight.