If you have the Ladder and walk downwards in an NES Dungeon type room, as the room scrolls, Link walks over the Ladder to cross even though the ground is walkable.
This has only appeared with the quest rule "Link drowns in walkable water" turned on. Turning it off right now fixes it for the current quest.
I've tried turning on and off various quest rules but it doesn't seem to change. With just the Link drowns in walkable water rule on from a new file, it doesn't happen though, so I would assume it's a combination of one or more quest rules I have turned on. There isn't much more I can tell sadly.
http://www.zshare.net/download/86225681fdbdc2d8/
This is in version Beta 18 as well.