I really dont understand why its happening. I have it all nicely set to X and character can still walk all over water and some walls. If someone wants to take a look heres my file.
It happens for example here or here
Because you have an invisible tile with a passable setting on top of it.
You have three layers in XP maps, each tile on any of these layers have their own passability and the sum of that passability is determined from top to down, not by visibility of which tile you can see.