OMG I had the same F***ing problem close to a hundred times now.
I dont really know how or what happens, but usually things are either half-stuck in the void, you have an opened wall to the void you don't notice, and even z-fighting.
You can check all of the objects, and if you see them half-stuck, move em, but it probably will still say "WARNING LEAKED".
The best thing to do is re-place everything. Erase the light entities, you, the shotgun, hell erase everyting. Then save (make sure to save after you run bsp), run bsp, and see what happens. If all else fails, do what I did and reinstall the whole fragging thing.