You can go back to the same location to finally get the navpoint but on 3 games, never once was I able to clear it from my journal. If it is the one I'm thinking of, SAM will say initializing or something and your expecting him to say stay in the area or more Kett to arrive but nope, that's it. Or it could be the one that you have to enter a sealed room. Even after, turning off whatever it was, nothing happened there either.
I think there are about 4 tasks that can not be completed. I have 2 games at 99%.