The most prevalent hit box problem in INS is headshot. Oftentimes, will people pull up their iron sights their model morphs a few inches taller and will look and fire over cover, but their hit box does not match their model and stays behind cover. It's even worse when said player is prone.
The second one I hear complaints about are with the shotgun. See, the shotgun has a spread shot, but if even part of it hits the game thinks the whole shell did damage. They'll pour gallons of blood all over the wall, but take relatively little damage. That's not as much a hit box problem as just a confusion of "How did that person's face just explode but not die.." The hit boxes are registering normally, the blood spray animation isn't.