Testing the SDAR at various ranges and depths I discovered some submerged units, diver or any other unit with loadout edited to breath underwater, refused to take any damage.
It seems that if a submerged unit is prone, and near the bottom of the water or an object for some reason bullets simply pass through them.
Submerged units 'standing' or vertical seem unaffected by the issue.
From further testing it primarily seems to affect targets being shot at from the same plane, side, front, or rear. Attacking from above or below can have bullets pass through legs and arms, but bodyshots and headshots can kill the unit inconsistently.