I've had this bug occur twice in the last 24hrs (that I've noticed).
MCPE 1.0.1 on Android Tablet.
Both times valuable single items (Diamond Pickaxe with Fortune II, Efficiency III and Unbreaking III, and Bow with Power II and Unbreaking II) disappeared entirely whilst I was sorting inventory/chest contents and/or doing some smelting. Both times, the item involved was in the hotbar when I opened a chest/furnace screen, but had vanished when I closed it.
Having this problem in all my games (survival) in MCPE 1.0.5 (via Amazon Appstore), on Lenovo A5500 Tablet.
Problem started immediately after updating from 1.0.4, and affects all worlds/games, regardless of whether they were created before or after the update.
Generally affects 3-5 slots of the hotbar, cloning items between those slots. Using/placing an item from one stack reduces the count in all cloned stacks. Opening a chest/furnace interface often changes the item shown in the cloned spaces, but which spaces are involved tend to remain unchanged.