Just had a game on a 80% water planet. My starting position was in deep water (dark blue). I couldnt build any of those metal spots in dark water. Only on the land, shores and light blue water. Is this a bug? My opponent said he experienced the same. Didnt know of that til now.
I think you have to click next to the spot so the "drill" coming from the extractor reaches the metal. The 3d perspective makes it hard to see.