I had a similar issue once where my quest progress wasn’t counting, and it turned out the ores I was mining were in a claimed area, so they didn’t register. What worked for me was making sure I was mining in an unclaimed area. If that’s not the case for you, try relogging or even switching servers for a bit. If it's still not working, I’d recommend submitting a bug report to the admins—they might be able to help you out and reset your progress.