On the "ice freezing water" comment, not necessarily. Think about putting an ice cube in a glass of water.
That said, if anyone knew what ice can do to rock (specifically, expand in cracks between rocks until the rocks crumble), you'd know why I'd say Ice's weakness against Rock-type moves doesn't make much sense.
Also, no logic I can think of can come up with an explanation for how Bug-types do twice as much damage to Dark-type Pokemon. Anyone care to explain this for me?
Thirdly... How is Ground strong against Poison?
And what about Ghost's resistance to Poison-type moves? I mean, they're already dead, so how does poison affect them at all?
And Bug's resistance to Ground-type moves? Seriously, if a bug was tossed around by an earthquake, what are the chances of it surviving?