just by happenstance I found in trying to clear the bug on my end that a quark process went off and seemed to be the culprit. essentially the bug is simple; a torch in the offhand randomly is assigned a blank NBT tag, causing it to not stack with newly made or broken torches. error was reproduced with saplings.

I suspect this has something to do with the way quark refills your offhand with items when a stack runs out. when trying to clear my testing inventory of the bugged torches, I had the auto-refill trigger and push saplings into my offhand slot and these have the same blank NBT tag causing the same behavior of not stacking when broken or new saplings are picked up.

Honestly, this is my closest lead on this error. I could be wrong in assuming its quark; the error could have been inventory-wide as a background process and quark's glitch with the torch and sapling just makes it appear it might be the culprit.

checking the items in game data using Crafttweaker yields no results beyond normal data background and a single normal tag from Minecolonies that is shared with items that do not have the error. I could only find the error examining my save through an NBT explorer/editor program.

if any more info is needed, simply ask; would be happy to provide. I wanna be free of this headache. this has been a bug I've been chasing since around 1.13-ish. it comes and goes with different versions it seems. none of the others in the pack dev discord have a clue what could be causing it.