I "removed" 3 remaining toolkits from one of my crates, there was a statement that let me know they were removed, the crate is gone but the toolkits are nowhere to be seen.
Was the crate on you, or on the floor? I know it happened when I did it with it on my back, but I thought Sin had set it so you couldn't do that. Otherwise, bug base it.
I got something similar to this. I crafted two keycards with a general event message of success and an inventory event to match for each one. Though the keycards are nowhere to be found and do not even show up in my inventory.