This is actually 2 bugs I think so I'll start from the beginning.

 After building this massive filing draw that opens and closes using 21 command blocks running /clone commands, I noticed that these phantom shadows were appearing on the floor after the drawer retracts (bug 1). If I stand in the shadow area, you can see that the area is shaded because the item in my hand is dark, then if I go upwards, I eventually ping into the light when I go above the bugged area.

 Then I found that by using /fill command in the effected region using WorldEdit with either barrier blocks or string, the region fixes itself and the shadows disappear, but when I try to get command block to do the same thing, it just doesn't happen (bug 2). When activated, the command block says that the last command was successful, but it's clearly lying; no barrier blocks (or string for that matter) will spawn in the area and the smelly shadow is still there. Its really ruining the build.