Why are some movies so dark (literally)?

Some of that is due to day-for-night shooting. Movies take a ton of light, and it's very easy for scenes to be dim and shadowy. Early on they figured out that they could film during the daylight, but not light it properly so the scene appeared to have been shot outdoors at night. Saves a ton of money -shorter production day, less use of electricity, crew, etc.

Another part of it is the way televisions show black/darkness. The modern LED TV prides itself on rendering the blackest of blacks, which was traditionally hard for televisions to do. The result is that what was dim and shadowy on a movie screen can be just plain black and hard to make out on today's television screens.

Stigmata was visually dark and had more running, dripping water outside of an aquatic-based film.

Bad cinematography

Maybe the success of the Nolan Batman films have something to do with it.

Clint Eastwood's early movies were insanely dark. The barroom scene in Outlaw Josey Wales is nuts.