I have provided a savefile for the Cheathappens developers should this prompt an investigation. The game just doesn't seem to create a proper bone charm with traits as it should. It could either be a problem with the game or the trainer, though it does seem as if the trainer allows crafting of some sort.

It will say you have no bone charms at all to equip. It will not appear under the Crafted bone charm(s), and if you have no bone charms at all then you cannot even navigate to that menu either. This results in a bone charm designated 'Unnamed' and it will just vanish.

you cannot craft another bone charm using the same trait. However, once you have crafted a bone charm with said retrieved trait 'one time' with either 2, 3 or 4 traits. It works the first time when you have sacrificed the bone charm of your choosing to retrieve its trait. I can also confirm that there is a problem when crafting using the trainer. There is a second category for crafted charms when your equipping them at the top

It's as if the game let you craft but doesn't give you anything after you craft the bonecharm. However, the bonecharms that is crafted doesn't appear and thus cannot be equipped. Unlimited Whalebone does make the whalebones unlimited, and let you craft bonecharms.

Dishonored trainer on cheats happens