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I have seen a few unfilled in triangles which mean that there is an unfound location. One was near 3 Maries cave. I literally went into TCL and cannot for the life of me find what I think I am supposed to. It was near Mary’s cave that I found that I was able to enter Mary’s cave and exit it without ever triggering the fast travel spot. I later walked by it and BAM I got it. Weird. I have one survivalist cache left to find and am annoyed at not finding it.
If you stand by the entrance to 3 Mary’s and look NW you can see the survivalist triangle as open if you haven't been there. As you move closer to it another triangle father away will "overwrite" it. If you go back and forth it will appear and disappear, you can see another triangle popping up just as the one you are trying to find disappears, tested this out extensively. It happens to the caterpillar mound and a couple other places. Once I found the survivalist on my own, went back to 3 Mary’s and the triangle was solid showing, but still got overwrote by the same triangle on the right side of the compass Somehow the location indicators are overwriting one another on the compass.
Here I just wish to add something in this case. You could look stuff up at Fallout.Wikia.com if you really can't find it. Some of the locations don't seem to have anything other than a nice view and have very small location triggers, so they're really hard to find. Currently I can't find the Yao Guai cave. Found it, I was being confused by a marker I'd placed myself. Sometimes I wonder if I'm bright enough to play this game.
Memory is a bit fuzzy but from the bridge nearby, goes right without crossing it. I think there was a path to it along the cliff. Also some locations don't show the empty dots even if you're 2 feet away from discovering it. Red Gate was one for me. I was circling the Survivalist's Rifle for 10 minutes straight. Then I got frustrated, TCL'ed and went into bird's eye view. When I got near the skeleton the discovery message showed up.
I have had the similar trouble. I have gotten a disappearing/reappearing blink on the island sort of north of the campground. Since it's happened on both playthroughs, my guess is it's always going to be there. Somebody probably just mistakenly left in a map marker after a location was removed. I had trouble with a place near Three Mary’s, it was called Red Gate and houses some very nice things, the triangle would appear as I moved toward it then suddenly disappear and not return until I was far enough away.
I had a lot of bugginess with the minimap thing in this game. I often did not get the empty triangles, and one time I told Waking cloud to wait, and she didn't show up as a friendly on mini map. Took me forever to find her again. I am playing the PC version by the way. I just wanted to say they aren't bugs, there are locations out there. But some aren't easy to get. Sun Sentinals, The Aerie, and Red Gate require you to find a path up to the top. Neither of these locations showed up on my mini map as an unexplored location. The Aerie and Sun Sentinals doesn't have a lot there except for a good view and some plants to pic.