For me the only time I got counts towards this achievement was killing Warmonger employees that were inside or located with the Warmonger Factory on the Planet Dagan.
This is the structure with an exclamation mark against it on Planet Dagan and is where the Dragoon prisoner is being held (since the latest patch that is). It opens at night once the nearby Warmonger employee is defeated.
I don't believe any other Employee type, such as machinist counts, well it didn't seem to for me. Had similar issues with Syndicate Gangsters too.