That's really weird. When I breed a mon that has some egg moves, I always make sure that move is on the last slot in order to prevent it from getting replaced by the newest move learned. In fact, the newest move should replace the first one in your moveset and not the last one.
Is your Murkrow also being put in the day care in order to breed again? If that's the case, you could just try to level it up enough, that way he won't level up as much while being there. You'd also need to check every now and then, and in case he's almost reaching a level where he would learn a new move, you then proceed to use a few common candies on it (this would be only a temporary fix though, what you explained should not be happening).