Apologies, my report missed so much useful info! I was running it via the itch.io app (ie installed via the app and using it's launcher) on Windows 10. I'm not sure if the phantom ores disappeared when quitting and reloading without having smelted them but the bug stuck to that save. I have reset (because it turned out that I had indeed missed that once having chosen leatherworking - and having regrets - I could not then go the no leather route!) - I had thought I might be able to continue and just not use that shop but apparently I was missing out on a whole bunch of consumables! (Though that didn't stop me "finishing the game" without actually reaching the water - I managed to collect all the achievements that don't require reaching the water, get all the turtles, equipment and accessories! I also had 999 copper ore and was afraid to smelt more incase of a rollover bug! ;) - which I then didn't test before resetting because I forgot! :'(
Having reset I can tell you that I don't have the bug any more and it seems that it was linked to the save file... possibly because I was still smelting when I quit? Not sure... I generally used to add ores in and start the smelt as soon as I returned to the surface to get them done while I did other things... but that included quitting as well as returning to the surface (copper), so maybe? It's a bit of a pain so I'll try to cause it again once I've completed this run if you don't mind! I have avoided having the furnace running when I quit this time around and have yet to recreate the bug... but that probably doesn't mean much! *shrug*
Thank you again for such a great little game as well as having composed such addictive music! :D