I am at the third cave. It shows that I have 67% chance dropping Stone, 25% chance Copper and 17% chance dropping Tin . 67 + 25 + 17 = 109% But sometimes I still received nothing . That's so weird. Maybe a typo, 57% Stone?
This is not a typo, the chances does not sum to a total value, means you can still receive nothing from that.
Based on the data you provided:
- First you have 67% chance for getting Stone.
- If it fails, you have 25% chance for getting Copper.
- If it fails as well, you have 17% chance for getting Tin.
If you didn't receive Tin as well, you get nothing.
I hope you understand

It means that improving the stone drop is actually nerfing the rarer components drops? it seems very punishing from a user PoV. Shouldn't drop rate be computed with the rarer first ? (thats how most RPGs compute drops for example)
If it stays that way, we could use a "sell" button for upgrades. Also, could we know what's the relation between increased drop rate upgrades and the % drop rate in a cave. Is it a flat 1% per level ? A proportional 1% compared to the base drop value ? something more exotic? Its hard to decide whether an upgrade is interesting w/o that kind of information