So far I've only been able to reproduce the bug on SMP, on my server, game.minerealm.com. The anvil allows tools to be combined with enchanted books, but upon closing the GUI, the original materials are dropped and the experience is seemingly gone (It can be recovered by relogging or by picking up experience in any way)
Steps to reproduce:
1) On a multiplayer server, combine an enchanted book with an already enchanted tool or weapon.
2) Move the item into your inventory and close the GUI.
Multiple people on the server have experienced this issue.
Duplicate of MC-1907.