Seeing a lot of people (including myself) that were having issues with this, until I found a solution that started working for me. The hatchet wasn’t registering stealth kills on a Super soldiers, until I switched to a knife (Weapons screen, scroll to the bottom, click on melee, pick any of the available knives.. You may have to buy one with silver coins)
Start on Brother 3 Research & Development map, there’s usually a Super Soldier that spawns directly on the street as you come up from the metro station (look left at the intersection) and/or down in the ditch below. There’s one that can also be patrolling the bridge by the statues to the right of the street. Camo yourself, stab him when no one is looking. Quit and reload. Hope this helps someone!