What is an Essence of Fate?

Solution 1:

It's an alchemy ingredient. You couldn't find it, because you didn't look in your alchemy pack.

It's sometimes created, as you found, by unraveling enemies via reckoning mode, and it can also be harvested from certain plants.

Solution 2:

According to this:

An Essence of Fate is used to create any of the ultimate potions. This reagent is exceptionally rare, and usually acquired through quests.

The page also directs to a list of master potions you can make with these essences.

I don't actually own the game (yet), but perhaps potion crafting reagents are not listed in your inventory, but somewhere else?