NBT Tooltip has been used to inspect the item metadata (in-game) and the below screenshot is from NBT Explorer.

playerdata.zip

Not even sure on what mod could do this.. I'll look into it.

Oh no... this looks like what NBT Crafting used to do anytime you put something in a crafting slot...

Not pointing fingers, but I am potentially providing a place to start looking.

Yeah I keep having this problem with my game, 10% of my items are duplicates of another of the same item. It's very obnoxious. It happens a lot especially when trading with villagers.

I have no idea what’s the cause, I’ll look into it.

I've also seen this happen with wheat after feeding cows.

Just to chime in too, it happens with torches and I believe it's when different wood is used for the sticks but not 100% sure if that was one of the causes.

It also happens with seeds and wheat.

It also happens with villager trading. The emeralds you get from villagers, sometimes cannot be merged with old ones.

from what i've seen droping items and picking them up should cause them to stack

torches as well - ones I picked up are different from the ones I crafted. I had to create a bunch of torches, place them on the ground and then pick them back up.

fixed