I've been to every nav point in troy . Do I need to leave the system and come back or something?
The mission was

kill pirate and I've killed about 6 so far on the various nav points I was supposed to scout for "Pirate"
I even went to places that weren't on the nav suggestions
I've been everywhere killed several pirates
Go to Troy
Go to War
Go to Pendelum Star.
Kill Pirate

and the mission won't complete.

I haven't landed between nav points.

and I've been looking for about 15 hours off on and on.

My strategy has been
do second mission then check every nav point on map
turn in mission
rinse repeat

This is my first Wing commander game so is there some concept I'm missing here?

Was it a bounty mission or a scout mission?
If a scout mission you have to go near the nav points requried by the mission (less than 1km) if a bounty mission it measn you have to scour each nav point of each required system until the pirate shows up and blast it to kingdom come.
You can check the requirements in the navmap by selecting "missions."

This sounds like a Bounty mission, since it gave you multiple sectors to search. In bounty missions, you have to kill a specific pirate or retro, any others you chance upon on the way don't count. So the best way to go about it is to to search the sectors it tells you to, and check your Nav screen whenever you kill what you were supposed to kill (a pirate in your case). If it was the right one, the mission description color will change from bright red to a faded red, and you can land to claim your reward.

Usually the target tends to be alone, while there are more in random pirate and retro encounters.

Also, in my experience, the bounty targets tend not to be in the first system mentioned. So if the mission goes like 'Pirate wanted in the New Constantinople system, may have fled to Junction or New Detroit', I would start by searching New Detroit and Junction first, and start with the smaller of the two systems to eliminate it. Also, if you have to load the game (due to having gotten killed in all likelihood), I believe the target is still in the same location. So if you died after finding him, you at least don't have to search everywhere again.

Hope this helps :)