When prone, the gun is held at an angle parallel with the ground, which messes up aim and zeroing. A trained soldier would never do this, as it messes up the zeroing of the gun, particularly when using scoped weapons [with 3d reticles] at longer ranges.
The same also applies when standing and leaning, the gun is held at an angle, although this is less of a problem as this is usually done at short ranges, where there is less error.

This has been an issue for a long time, and breaks the useablity of sniper weapons at long ranges, as it becomes impossible to aim accurately.