When you say "set of waypoints", do you mean the "search pattern" function?
I think that is only there to make it easier for you to search an area (I haven't used it myself since SH3 and I haven't had any missions I couldn't complete).
I still think that you problem is that you didn't spend the full 48 hours within the radius of the binocular icon. Load up your game and check the mission status (press F12).
Edit: the patrol icon will turn gray on the "F3" map when completed.
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