Version: 5.9.4
MC 1.21.1

Included in FTB Skies 2 v1.2.0 with these addons:

Steps to recreate:

1. Click a T2 spell book onto table
2. Select some spell. Then press Select button. The interface will close.
3. Open again and select another spell. Repeat step 2.
4. You will randomly drop the spell's required item as a item inventory, even when not having it in the first place.

The process is somewhat random, you may want to try the same spell more than once or just multiple spells.

Seems to work best with Extract enderpearl dupe

Are you sure it is actually duping the items and not just pulling them out and refunding them? I cannot recreate this. The scribes table automatically pulls items from nearby inventories remotely.

Oh that's why. I think i had it near some chests. Will reopen if I encouter this again.