Multilevel geometry is only supported in the form of multiple grids stacked on top of each other.
In a single grid everything inside its bounds is seen top down, literally. So for any given grid cell, if an obstacle exists in the space between the upper and lower bounds, that cell is blocked.
The simple fix is to not have objects that should not be considered obstacles in the obstacle layer. That of course only works for the single grid scenario.
If you actually want multiple levels on top of each other, you need a grid for each. Refer to the examples project for an example.