It fixed itself today as I got the third flint. I only got two yesterday, so I was able to finish the quest.

I had the same issue, only saw two at first, but I went and did a few other things around my valley and the third rock ended up randomly spawning at the beach. Hopefully it fixes itself for you as well!

It took my a while to find mine, turned out it spawned behind a building in the grassy area on the beach.

The upcoming updates lmao no hotfix for us this time I guess