Reported in Angel's Refining: https://mods.factorio.com/mods/Arch666Angel/angelsrefining/discussion/8116

Crystallization from crystal seedling and crystal catalyst to gem ores 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