This is a long-standing topic on the forum. I've been seeing it for years and years. I have seen it happen maybe twice with my iTunes and I am still using iTunes 7.5. However, there is nothing definitively pointing to to it being a specific issue with iTunes. In the past I have created and deleted hundreds of tracks in a day and who knows if my computer's operating system or iTunes slipped up somewhere, or even if I did in selecting files for deletion. The other question is, is the media file itself also missing or is it just the entry in iTunes that is gone, or is the link broken? With something this vague it's like going to a car mechanic and asking them to troubleshoot a "strange noise" that happens maybe a few seconds for every 20 hours on the road and not being sure where it originates, nor if it has something to do with the road conditions, or the fuel in the car, or the engine, or the tires, etc.
Keep backups. The two or three times it has happened to me in the last 8 years the original file had gone missing but the entry was still in iTunes (broken link). I periodically run one of Dougscripts Applescripts to check my library for broken links and I was able to rescue the file from my backup before I overwrote the backup. I try to do this each time I backup my library just to make sure I don't overwrite a good copy with a bad copy. Of course this won't work if the entry has also been deleted in the library file but I manually manage my library and this has the mixed benefit of iTunes not automatically deleting the media file when I (or it?) delete the entry in the library database.