Well...I've already got the first bug. Looks like it wasn't fixed when I mentioned it in the last thread...
As you can see, Link can still swim over solid tiles.
If I'm understanding it correctly, the brown tile means that it's a water combo with a solid combo on it. (on another layer):
http://img833.images...0/zelda003c.png
Those are the ones he can swim over, even though they are indeed solid.
All right. I'm pretty sure that's the correct behavior, since it's normally the combo type on layer 0 that takes precedence. In any case, it's been that way at least since 2.10, which makes it hard to change now. (Plus, of course, making changes to walkability handling is really hard, especially where water's involved.)
So yeah, not technically a bug. What you can do though is do what LTM said, or just make it completely solid, with no water on layer zero at all. Why does there need to be water on layer 0 anyways?