Upon getting far enough away from a chunk, causing it to unload (improperly) (my guess), the chunk resets its lighting level to 0 (sometimes to 15 in very rare cases) regardless of any light sources around. Placing blocks in the chunk do not update the lighting, only removing and replacing the light source itself updates it, but only for the area that it lights up. To get all lighting back to normal, one has to go to every light source in the chunk and re-place them.

Those areas, even for places right next to torches, allow hostile mobs to spawn.

Issue is server-side as F3-reload doesn't update the lighting back to normal.