As the title says, if you open your baubles inventory with the hotkey somehow there's 9 iron nuggets in the crafting slot. I don't know how this is happening but it is super weird

Wait, how is your player crafting area 3x3? Or do you mean the output slot?

I've been doing a bunch of research and looking at the game log. It seems that this happens whenever a mod does not properly import an oredictionary item. baubles thinks since it is an invalid oredictionary item, that it has no recipe, so it give it to you for free. Happened to me with forestry one update and once they fixed the invalid oredict, it was fixed. So it's sort of a bug with baubles, but it is also an issue with other's mods.

I'm having the same type of issue (same problem, different item). There is a Thermal Foundation Copper Plate in the output slot on the Baubles inventory screen.

If I take the copper plate out, go back to my inventory and then re-open the Baubles inventory (using either hotkeys or manually clicking the bauble icon) another copper plate appears in the output slot.

Still trying to research which mod conflicts are causing this.

Minecraft: v1.12.2
Forge: v14.23.1.2604
Baubles: v1.5.2

Done a bit more testing and it's not just the Baubles inventory this effects so my issue is not related to Baubles specifically.

Update: In case anyone else wants to check, I just fixed my issue. It's related to the "registerNewCraftingIngredientsAsItemStacks" option in UniDict. Setting it to TRUE was causing the problem. Changing it back to FALSE and my issue went away.