I hit a protected Yanmega with U-turn.
Thank you for pointing this out, but please note that it is much easier to keep track of bugs if you post them on the tracker:
http://sourceforge.net/tracker/?atid=919095&group_id=186888&func=browse
With regard to invalid teams, every time we've heard it before, it's turned out to be invalid, or an old team. Perhaps you forgot moves on one of the pokemon. If not, you can attach the team to a bug report and I will look at it (you can save invalid teams).
If anybody's curious about progress, the list has been updated. I completed substitute yesterday, which was probably the last move that is both complex and good.