Purely anecdotal, but it happened to me. I had ripped (using iTunes) about 200 CDs I own, over the course of a couple of months of throwing in a CD whenever I wasn't doing anything too important otherwise. These 200 CDs were joined by about 10GB of legally purchased MP3s from sources other than iTunes. In fact, I've only ever bought two albums on the iTunes store.
Anyway, some time after I had ripped and cataloged all of that old music, I decided it might be a good idea to back it all up to an external hard drive for safekeeping. I hadn't really paid much attention to file sizes or anything, but I knew I had about 36GB total. Curiously, after copying to the hard drive, I saw I only had about 25GB on there. This was too big a discrepancy even knowing I hadn't really looked at my library before copying. So I dug in, and I realized that the vast majority of MP3s purchased online were missing completely. There was an odd song here or there, but there wasn't a complete album (and I almost always buy the whole album in MP3 format) either on the backup or in iTunes itself. From what I could tell, all of my ripped music was there, but it was as if iTunes decided to "forget" that I also had all those purchased MP3s, and somehow had deleted them from my library without asking me.
Further investigation revealed that the few remaining MP3s were all available in the iTunes Store for purchase, and almost all the missing music was not available for purchase from Apple. It's mostly indie and obscure stuff so that in itself isn't surprising, but I found it intriguing that iTunes somehow deleted music that it couldn't have sold me. I honestly think that's more coincidence than anything, since a small percentage of the deleted music was available from Apple at the time, but it was frustrating nonetheless.
The story has a happy ending though: I had previously backed up my purchased MP3s onto DVD-R media, so I never actually lost anything. But that was the last day I ever used iTunes for anything.