I farmed and bought materials to make 2 Radiance II rapiers, the first and second tiers of both were to be Holy and Flaming burst. While making the very first item (inferior focus of positive energy) I placed my stack of small gnawed bones, small sulferous stones, small devil scales, small arrow heads, and low energy cells in the machine. I was able to craft 1 inferior focus of positive energy, but my stack of small bones and small arrowheads were stolen by the machine. They are no longer in my ingredients bag and I have tried the steps people are taking on the forums for lost ingredients.
(Edit: the amount of small arrow heads and small bones were 4 each in the stack, this may help in solving the problem)
This may be able to be recreated by attempting to make an item with numerous parts from inside an ingredients bag.
I submitted a ticket and apparently the items aren't showing up as destroyed even though they are no longer in my bag upon logging out, searching, turning on and off gather, moving the bag around to bank and back into inventory.
At the very least, if this is happening, players should be notified. Regardless if it's not showing up in your logs, it happened. It's not like they are items that are incredibly expensive to most players, but the fact that they were mine, I spent time and plat acquiring them. I am a new player, barely here for a month, and I feel very wronged by the fact that I was told to simply submit a bug. I have already put real money into the game and plan on putting much more in for TR and packs and even VIP should my situation allow it in the next couple of months, but honestly, being told "I can't help you, write a bug" is NOT a way to keep a customer. I paid for a service using this real money and expect real support in solving an issue.