I completed almost all points in the second area and indeed I found 2 points that can't be completed.
One doesn't turn grey, an the other just keeps remaining a ? even after completing it.

:/

I'm on my second run-through and haven't found any points I couldn't clear. In reference to your issue with the spider nests in the caves with Keira - you don't blow them up, like other monster nests - you burn them.

There are a number of points which are not at ground level. Most likely there is a cave nearby that you have to enter to find the point underground...

Not in my case. One is on a really flat shore. I checked everywhere and there is no other chest to loot to grey it out.
The other is an abandoned place I already completed. NPCs and merchant are there, but on the area map you can still see the very white ?