Confirming this bug, though it seems to potentially be coming from ShinyBob.
Crystallization from crystal seedling and crystal catalyst yields the wrong products for 4 of the 6 recipes (amethyst ore and diamond ore yield the correct products).
Incorrect products:
Crystallizing topaz ore -> emerald ore
Crystallizing emerald ore -> sapphire ore
Crystallizing sapphire ore -> ruby ore
Crystallizing ruby ore -> topaz ore
First few lines of ShinyBob's locale\en\bobsplates.cfg:
[item-name]
ruby-ore= Topaz Ore
ruby-3= Raw Topaz
ruby-4= Cut Topaz
ruby-5= Polished Topaz
The rest of the definitions match the patterns listed above.
In-game results: https://imgur.com/a/YxuxB