After you win the war for either the Stormcloaks or Imperials, and they tell you that bands of the enemy have setup camps throughout Skyrim and to destroy them, what are you supposed to do? I've found a few camps, clear them out, but can never kill the Legate. Why is this, and what is the point?

Are they saving the legates for some future expansion?

The Essential Tag is not removed at the completion of the Civil War.

Now, I just avoid those few camps when I come across them.

I believe its just a miss-placement of a essential NPC, But, You can just leave them there after defeating them, they wont hunt you down lol

I don't know whether they will be in future expansions but I think it's just an error with the essential tags not expiring.

And when in doubt, use the Spoilers Board