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,
(Edit) 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, go 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 feets 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.