The examples I gave in 1 and 2 are because path finding can't cross that door.

With the level editor I found the door is placed from the middle of a cell to
the middle of the next cell.
Removing the door does nothing, but moving the wall so a cell if free takes care
of the examples.
I think there were other places with the same problem, don't recall which, it
might be the same for them.

So either enforce a grid layout or teach pathfinder.c to generate paths that are
not grid aligned. (maybe use the Theta* algorithm?)