Mechanic

Soul Bottle

For the most valuable and dangerous mobs (see the full list), a plain activation item isn't enough. You need to capture the mob's soul by really killing it at least once.

Crafting an empty bottle

Glass Bottle + Soul Sand

How to capture

Carry the empty Soul Bottle in any slot of your inventory.
Go find the real mob (a Wither Skeleton in the Nether, a Guardian in an Ocean Monument, etc.) and kill it for real, out in the world.
On the kill, if you're carrying an empty bottle, it automatically becomes a filled Soul Bottle for that specific mob, with a confirmation message and sound.
Place the filled bottle in the matching farm's activation slot.

Durability

The filled Soul Bottle follows the same rule as any other activation item: good for a limited number of production cycles (64 by default) before it runs out. After that, just capture another.

Visual

The bottle's model swaps automatically between its empty look and a glowing, essence-filled look once a soul is captured.