I've had a recurring issue where I'll get a mission to go kill "x" targets, where "x" is either bounty hunters or authority ships. The first time I did it, the game didn't recognize that I had killed two security vessels - until I logged out and back into the game...THEN it recognized that the mission was completely and allowed me to turn it in. Recently, I killed two bounty hunters and even after restarting the game, it didn't recognize that I had completed the objectives and it wouldn't allow me to turn in the mission.
How do I know that they were bounty hunters? Because both of them scanned me and said "all clear, pilot"
How do I know that they were bounty hunters? Because both of them scanned me and said "all clear, pilot"