NPC stations steal ore out of Ship Drills.
Happened to find an Iron Ore outcrop shortly after accepting a Contract. After docking I got an error that my ship didn't have the required items. All the ore and most of the stone I had mined had vanished from my ship.
Eventually I found the missing materials in the connector on the NPC station itself.
The ship I used is the Scout Miner which is around 750,000 SC , bought from the station. If you do decide to alter this ship, make the ejector at the back default to off, it's annoying if you want to mine stone.