The funny thing is, it happens when iTunes is open and apparently not doing anything.
I have iTunes open on a 2nd monitor. I had listened to a couple of podcasts that were on my unplayed smart list earlier. This feature is broken from earlier iTunes, in that I have to select each podcast one at a time instead of having them all play. When I was done, I continued browsing on my main monitor.
After a while I looked over to the other monitor, 3 songs and a movie are now listed as unplayed, even though they have been played lots of times (well the songs have been played lots of times).