I had this problem occasionally with GC1, but it seems to be worse with GC2 beta 3: I select a ship, right click on a destination, but the ship heads off to some unknown destination of its own. Right now, I've got a colony ship which simply refuses to head toward the planet I want to colonize. Each turn I left click on the ship, right click on the planet, only to watch it continue to move in the opposite direction. When this happened to me in GC1, I was able to correct it on the turn after it happened, but it's been 6 or 8 turns now, and this colony ship is still ignoring me.