I've noticed this happen in two different situations so far.
1) When I spin flax into bowstrings, one of the flax that's supposed to turn into a bowstring disappears.
2) I was crafting gold bars and sapphires into amulets and noticed that one of them disappeared as well. I don't know if I got experience from it but this obviously shouldn't happen. It could happen to every inventory, it may even happen more than once per inventory.
EDIT: Happened 4 times so far the past hour.
Side note: When you cut a gem not named opal, topaz, and jad, you still can get a crushed gem. I posted a thread about it but it has not been fixed yet although James posted on it.
http://www.runerebels.com/smf/index.php?topic=4171.0No responses on this thread either about knives being slow.