This one will take some explanation to convey. But a picture's worth a thousand words!
This pic demonstrates two bugs:
1) You can see that Link is, like, going through the solid tile. I guess when Link is in water, Link ignores the solidity of the half-stairs half-solid combo.
2) While walking in the stairs, Link is walking above the water. He should be below it.
Then there's this weird third bug. With "Cap FPS" off, if you enter a door similar to the one above, quickly exit, and try to get back into the water, Link will actually go back into the stairs. You might need to play with this one to recreate it, but it definitely exists. It's like this:
-> (try to go any further) -> 
If you're having difficulty with this one, I'll gladly make a video.
Some of these bugs may relate to the fact Link swims too slowly.