When enchanting an item (in my case a pickaxe), and enchanting a second afterwards, the enchantment of the first item disappears. To reproduce:

1) put a item into slot 1, put lapislazuli into slot 2
2) select an enchantment and enchant
3) tap the enchanted item - it will disappear from the slot

If you exit the table at this point, everything is fine - you can pick up the enchanted item.

4) select a second item to enchant into slot 1, put lapislazuli into slot 2
5) select enchantment and enchant
6) exit the table

Result: experience levels and lapislazuli for both levels have been substracted.

There will be (on floor, or in your inventory) 2 items:

Item 1 - bare, unenchanted.
Item 2 - enchanted as specified.

A similar bug seems to hapen at the anvil, i haven't reproduced that one yet.