Weird Missing Passage Blocks[Mapping(?) Problem]

[Kaleidx]

Alright, my question is pretty general and I haven't quite seen a problem like it around so, I'm guessing there's a small percent chance the error is with my comp or something.
Anyways:
I seem to be coming up with a really random and weird problem which I hope I don't feel dumb if I find a simple resolution to it. It seems this happens when I begin creating the tiles, etc, on an empty map with no events or anything whatsoever.

Say I made a small square patch of grass tile and a little river running through it. When I playtest it, i walk up to the river to test if it looks and stops the character where it should before they walk over it. Yeah, everything works fine. Before you think the obvious, yes I did set up the x on the tile passage on the said tileset. It's just like, on a certain(I think mostly random)part of a river that the player can walk right through it and over previously unwalkable water tiles to a certain point(like an invisible maze). All the tiles were also on the same layer. This has happened a few more times on different parts of the map such as when I make buildings or fences - it's just certain parts of it when you can just walk through it. I couldn't for the life of me find out why so I just tried hiding these 'ghost' spaces by just adding more block tiles to mask it which seem to work alright. But I was hoping to find a solution to fix this problem rather then continue masking it.
Again, I said it was empty beforehand and on the same layer.

If this helps at all:
http://i156.photobucket.com/albums/t30/ ... ample1.jpg[/img]
That is the only spot my actor can stand on in the water. It's the first layer so nothing is below it or above it and is all the same tile. So I can not move down or right anymore.

Any help would be appreciated. Request more info if needed.

 

[ZanetheVamp]

i would say just put the water on the second layer.

 

[Kaleidx]

Hmm, yeah, thanks! That seemed to have worked for the water but as I said I get the problem in other random areas where things are on the second layer with ground tiles below it.

http://i156.photobucket.com/albums/t30/ ... ample2.jpg[/img]
The red flower bush below my actor is on the 2nd layer with a floor tile beneath it. I've checked, rechecked, and checked once more that it had no passage access and sure it was the right one I was choosing but I can still go right through it and into the building 2 steps but nowhere else.

The building tile I used is the exact same as the ones next to it but I can't go into that one but just in that exact spot.

 

[Acera]

I had this problem as well (with the trees). I think it has to do with the database configuration (at least, it did for me). Here's a screenshot to show you:

Spoiler: I hate trees

http://i29.photobucket.com/albums/c260/Killer620/treesftl.png[/img]

As you can see the tree has an empty corner on the top right handed side. You should make sure that you have that tile on passable and on priority 5. That was the problem for me anyway.
Hopefully that was the problem, otherwise... Well than I don't have any idea on what it could be.
~Acera

 

[HarryE]

Yeah, by the looks of it you've probably set a tile there that is transparent on the second or third so you can walk on that square.

To check this, get a random tile from the side, then fill the second layer with that. If you have set a transparent tile by mistake, then it will show up.

To get the map back, simply fill with the top-left tile.

 

[Kaleidx]

Ah, yes of course! It seems at first I tried messing around with that tree by changing the priorties around but nothing really seemed to fix it. Then I tried removing the tree completely but that didn't work either.
But silly old me figured it out that I was using just a random transparent tile to erase mistakes on a layer. So I did what Bruno said and filled the whole layer with the top left square and it worked.
I think thats why changing the waters layer worked as well because I must've erase something there with a transparent tile at some point.

Alright, thanks for the help figuring out how dumb I am!
Fixed!