Poison should have be as effective against Water as it is against Grass in my mind. I mean, changes to a river's pH would severely affect species in it. As for Ground beating Poison, I assume that's because you have poisons in gases below ground, and ground acts to contain them. That's the best I can think of. (I always assumed Bug DID beat Ice 0_o)
Having Normal immune to Ghost also is something I don't always understand, and probably along with water-poison the one I feel most strongly about, since Ghosts can interact with ordinary objects and there's no reason an attack based on attacking things with said objects can't exist, like a haunting. It must be so that Normal isn't underpowered and screwed from the fact Normal has no effect on Ghost.
EDIT: Missed another discussed obvious one: I feel Ice should beat Water purely because the ice type can also be associated with cooler temperatures rather than just blocks of ice.