Video showing what may cause hit registration issues. It seems like if a target is behind an object, regardless of height, may cause line of sight issue for the bullet to not register.
Video here: https://youtu.be/nvhB58fwiPU
In the example in the video a infected does not register a hit in the head when they are behind a waist high object. Then maneuvering position where there is "clear line of sight" with no objects blocking the infected, the hit registers.