I think I am having the same problem as the OP except I save yt videos by going into my temp files folder. So far, I have noticed this happening with videos from one person's channel only.
Here is, for example, a 29-second video that I can't download:
http://www.youtube.com/watch?v=ReP9pN5jJDY
For longer videos from this channel, I see a series of 2,400 KB files in my cache that are unplayable.
Thanks in advance for any help.