I heard that other people had the same problem before, but I wasn't able to replicate it or pin down the cause. Is your save file old by any chance?
so, i actually wanted to ask this same question myself since i've got the same problem, but i kind of notice that i can't break any stones i've seen after i upgraded my pickaxe to copper pickaxe, it's impossible to proceed in the desert mine because of this, the only solution for me is to use noclip cheat to proceed, and no this is not an old save since i just downloaded it today here...
And by the way, what is the advantage of upgrading to copper pickaxe? i didn't see much improvement compared to old pickaxe tbh
Edit : So, i mess around with the game data and try to remove copper pickaxe and put back the normal pickaxe, it works! I can destroy the stones once again! So yeah, this is probably the copper pickaxe fault!