To solve that you have the "Colapse" mechanic, you are not supposed to go far in the first couple of runs. There is also and upgrade in the midgame that allows you to "control" the ore health.
There is the "Collapse" mechanic, but it's very far off for me. Even at 1.16K meters, the bar is only at 45K out of 1M to get a runestone. Choosing to collapse now says that I won't get anything for doing it. Am I missing something?