you aren't doing anything wrong. upgrading the mine changes the time it takes to do each round of mining for materials and at some levels change the selection of ores availiable. i found myself a dark mine with pulley is probably the best value for your buck for the dark mines which give stone instead of dirt and can also yield gems but if you want dirt and low level ores a simple mine with pulley is best usually i have both set up. I do wish the undeniable wiki site for hydrocraft allowed for player comments on each page that can be up and downvoted so this kind of information can be shared easier with players without having them to ask the same questions each time or find out the hard way.

The Dark Mine gives you some minerals you cannot get from the normal Mine.

Originally posted by Hydromancerx:

The Dark Mine gives you some minerals you cannot get from the normal Mine.

First of all, thanks for the answer Hydro. But surely, you can see the problem here. Say, you are after lead and sphalarite (to make zinc which will allow to produce brass). You can mine lead in a normal mine at a very fast speed, spending no resources but time and time only.
Then, you upgrade to the highest mine, spending millions of resources and you try to mine for sphalarite. You get a bucket full of water, you carry over a charcoal, you charge your miner's hat with batteries (you're overweight at that point) and you mine three times (at best) at which you run out of water, batteries and possibly your half spent charcoal. You will probably end up with 3 stones and MAYBE two stones and a high end mineral.
This mine is no way feesible. Maybe if it NEVER produced stone, maybe, just maybe it would be something to consider.
We were playing Hydrocraft with an unparalleled enthusiasm until that point. Now our PZ group believes that any high end recipe we go after will be a similar disappointment, so we just spawn in whatever we need with admin powers (including bullets). We were very patient with this for months and the gradual progress of how you needed to grind to make things really was entertaining. Not anymore.

Agreed, the Dark Mine With Steam Pull needs to be MASSIVELY given a Buff. It should NEVER generate plain Stones or Chipped Stones.

The normal Dark Mine is the best deal. Get a candle-based Mining Hat and a Pickaxe and you spend an entire day down there!