If you have played the tune in iTunes on your computer then the file has changed - play count etc. - during the sync if those same tunes are on the iPhone/iPod then iTunes is updating those files to reflect the current play count etc.
The same is true if you play a tune on the iPhone/iPod then it is updating the data in the iTunes Library.
You're probably right, I just never noticed this behaviour before so I was a bit suprised and curious as to why this was going on.
I still think it's strange, but since the sync of these "extra" tracks is relatively fast, it sounds like a good explanation since nothing actually seems to change on either unit.