Goddamned Bats: The leeches in Train Derailment, small spiders in Mansion Incident and the roaches in Raccoon's Destruction have the potential to be like this. However, only a small number of them actually attack, in which they cause no damage unless you leave them on, and can be removed with a simple swipe of the knife. It's mainly if you're overwhelmed by other enemies at the same time that they become annoying. Played straight with the crows.
Scrappy Mechanic: The player must replay certain levels and score an A rank in order to unlock the final level, adding an unnecessary layer of padding in the eyes of many. This was removed in The Darkside Chronicles.