I did get all three force stones, but only 2 of them remain in my inventory. Even before I sent this report, I checked the place for each stone and they were all taken, as I thought.
Blinky said I was missing 2 stones: the one at the lava area and the one in the water. I hadn't taken the lava one at the time, but I did take the one at the water in river ruins.
If you want, I can send screenshot of every place and my inventory, but I don't see a reason for such thing. Must be a bug that I'll just have to live with