When I was digging, I was noticing that there are just random light sources where they should be, here is a pic.
This is a core minecraft issue - Not EMC related. I am not certain on how to fix it; but I think you may be able to remove them by placing blocks where the light seems to be emitting from then breaking it. Note: there is no reliable way to purposely recreate these lighting artifacts. <- I think that is the correct word.
I know they were supposedly working on the lighting of minecraft. Presumably that would fix this issue.
They supposedly only "fixed" the black lighting spots in 1.5. I don't know/think they're working on getting something to fix it sometime soon. It could also possibly be a bug with EMC when there was originally a light there and somehow, something made it stay there when the residence reset.