Lighting/mob spawn glitches

Light sources (e.g. torches/fire/lamps) frequently don't provide the proper light levels.

Hostile mobs/monsters that typically only spawn in low light levels appear to be spawning in well lit areas. 

Areas with roofs, tops (e.g. leaves, cave openings, mushrooms) and transparent blocks often appear to be very dark or have sudden random block light changes. 

The lighting glitches typically happen during a certain game change, (e.g. traveling to and from the Nether or End, going to sleep, loading unloaded chunks, etc.)