gemstone ore no result.
tested against angel's and madclowns and bob's. only issue i've seen so far is gemstone ore doesn't yield "unsorted gemstone" per bob's ore config setting.
I think this is angel's ores' doing as it likely removes the ore field from generation and also probably removes the ore field result, but i'm not sure. i can send a modlist if that helps or try different arrangements of mods.

I'm not sure if the gemstone ore mining result isn't being saved during the data.lua run or if the way bob's ores is set up the result for the ore gets set after the saveOres function is run. not sure. not sure how to test that theory, either.

test 1: disable "unsorted gemstone ore" in bob's ore config. expected result: gem ore field should yield individual gem types [hypothesis: omnimatter ore deblocker runs data.lua before this config takes effect (IE: bob's ores may later remove the mining-result from gem-ore field and replace it with a single item, resulting in this error. Actual Result: no change.

investigated bob's ore's mod indepth. found that the mining result for gemstone ore is, in fact, declared from within data-updates.lua, (which is currently running after you run the save function within data.lua) meaning when the save-function runs, there is no mining-result to deepcopy.

Since the way bob's ore's has multiple methods/configs surrounding gem-ore, the only way to fix your mod is to include a special case for gemstone ore.

EDIT: uploaded solution below

i think the way this interaction is occuring also likely overrides the function that enables gemstones-from-other-ores to work properly too, for the same reason. so in a personal test, i copied/pasted most of bob's ores data-updates.lua into the end of data-final-fixes.lua of your mod to see if that would fix the issue, and it worked.

published my solution here: https://gist.github.com/usafphoenix/9262327f468ca7633f9a61d8099d42db