My filing system is almost foolproof, but occasionally CDs have vanished without explanation. Often I find them after grabbing the wrong stack as I conduct a periodic massive shift to file all new acquisitions (which often approaches 300 titles by the time I get to the Zs). But there are times when they are just missing and I definitely didn't sell them. I think that I may have left a CD behind in the studio once or twice, but I haven't been downtown to record my weekly radio show in over two years, since I've been producing it at home.
Perhaps the most frustrating is when my wife loaned our truck without asking me, removing a CD from the player but not the jewel box from the storage compartment. By the time I got the truck back, the CD was nowhere to be found to put back in the jewel box. About the time that I buy a replacement copy, it will turn up.