I've done it several times in CDs, but only once on DVD even though that collection is much larger. It was a John Wayne movie that I suspected I might already have but it was at a cheap price. When I got home I discovered I had the movie on a disc with another movie while the one I just bought was just the one movie. I have had the opposite happen, where I've found titles in my collection that I don't remember buying but they're on my shelves and logged in the software. Must be DVD gremlins.

It only happens to me with titles in PD collections, because I didn't buy the movie specifically on its own, I won't always remember...